Akaike information criterion should not be a “test” of geographical prediction accuracy in ecological niche modelling

Model complexity in ecological niche modelling has been recently considered as an important issue that might affect model performance. New methodological developments have implemented the Akaike information criterion (AIC) to capture model complexity in the Maxent algorithm model. AIC is calculated based on the number of parameters and likelihoods of continuous raw outputs. ENMeval R package allows users to perform a species-specific tuning of Maxent settings running models with different combinations of regularization multiplier and feature classes and finally, all these models are compared using AIC corrected for small sample size. This approach is focused to find the “best” model parametrization and it is thought to maximize the model complexity and therefore, its predictability. We found that most niche modelling studies examined by us (68%) tend to consider AIC as a criterion of predictive accuracy in geographical distribution. In other words, AIC is used as a criterion to choose those models with the highest capacity to discriminate between presences and absences. However, the link between AIC and geographical predictive accuracy has not been tested so far. Here, we evaluated this relationship using a set of simulated (virtual) species. We created a set of nine virtual species with different ecological and geographical traits (e.g., niche position, niche breadth, range size) and generated different sets of true presences and absences data across geography. We built a set of models using Maxent algorithm with different regularization values and features schemes and calculated AIC values for each model. For each model, we obtained binary predictions using different threshold criteria and validated using independent presence and absences data. We correlated AIC values against standard validation metrics (e.g., Kappa, TSS) and the number of pixels correctly predicted as presences and absences. We did not find a correlation between AIC values and predictive accuracy from validation metrics. In general, those models with the lowest AIC values tend to generate geographical predictions with high commission and omission errors. The results were consistent across all species simulated. Finally, we suggest that AIC should not be used if users are interested in prediction more than explanation in ecological niche modelling.     

Finding consistent strain distributions in the glenohumeral capsule between two subjects: implications for development of physical examinations

The anterior-inferior glenohumeral capsule is the primary passive stabilizer to the glenohumeral joint during anterior dislocation. Physical examinations following dislocation are crucial for proper diagnosis of capsule pathology; however, they are not standardized for joint position which may lead to misdiagnoses and poor outcomes. To suggest joint positions for physical examinations where the stability provided by the capsule may be consistent among patients, the objective of this study was to evaluate the distribution of maximum principal strain on the anterior-inferior capsule using two validated subject-specific finite element models of the glenohumeral joint at clinically relevant joint positions. The joint positions with 25 N anterior load applied at 60° of glenohumeral abduction and 10°, 20°, 30° and 40° of external rotation resulted in distributions of strain that were similar between shoulders (r2 ≥ 0.7). Furthermore, those positions with 20-40° of external rotation resulted in capsule strains on the glenoid side of the anterior band of the inferior glenohumeral ligament that were significantly greater than in all other capsule regions. These findings suggest that anterior stability provided by the anterior-inferior capsule may be consistent among subjects at joint positions with 60° of glenohumeral abduction and a mid-range (20-40°) of external rotation, and that the glenoid side has the greatest contribution to stability at these joint positions. Therefore, it may be possible to establish standard joint positions for physical examinations that clinicians can use to effectively diagnose pathology in the anterior-inferior capsule following dislocation and lead to improved outcomes.     

Clumping characteristics and hydrophobic behaviour of an isolated bacterial strain from sewage sludge

Summary A clump-forming bacterial strain was isolated from a sludge community derived from a waste water treatment plant. The Gram-negative bacterium is hydrophobic and forms an extensive capsule while clumping in dilute medium (0.1% bacto peptone). Emulsan, a capsule inhibitor, does not affect the clumping ability of this bacterium. Clumps are not dispersed with high and low pH, detergents or chelators. Bacterial clumping selected by the waste water treatment processes appears to be a complex set of interactions within and between the strains of bacteria. This study reveals some of the complexities.     

Machine vision photogrammetry: a technique for measurement of microstructural strain in cortical bone.

Understanding local microstructural deformations and strains in cortical bone may lead to a better understanding of cortical bone damage development, fracture, and remodeling. Traditional experimental techniques for measuring deformation and strain do not allow characterization of these quantities at the microstructural level in cortical bone. This study describes a technique based on digital stereoimaging used to measure the microstructural strain fields in cortical bone. The technique allows the measurement of material surface displacements and strains by comparing images acquired from a specimen at two distinct stress states. The accuracy of the system is investigated by analyzing an undeformed image set; the test image is identical to the reference image but translated by a known pixel amount. An increase in the correlation sub-image train parameter results in an increase in displacement measurement accuracy from 0.049 to 0.012 pixels. Errors in strain calculated from the measured displacement field were between 39 and 564 microstrain depending upon the sub-image train size and applied image displacement. The presence of a microcrack in cortical bone results in local strain at the crack tip reaching 0.030 (30,000 microstrain) and 0.010 (10,000 microstrain) near osteocyte lacunae. It is expected that the use of this technique will allow a greater understanding of bone strength and fracture as well as bone mechanotransduction.     

Strain and load thresholds for cervical muscle recruitment in response to quasi-static tensile stretch of the caprine C5–C6 facet joint capsule

The aim of this study was to investigate the response of cervical muscles to physiologic tensile stretch of cervical facet joint capsule (FJC) at a quasi-static displacement rate of 0.5 mm/s. In vivo caprine left C5–C6 FJC preparations were subjected to an incremental tensile displacement paradigm. EMG activity was recorded during FJC stretch from the right trapezius (TR) and multifidus (MF) muscle groups at the C5 and C6 levels and bilaterally from the sternomastoid (SM) and longus colli (LC) muscle groups at the C5–C6 level. Onset of muscular activity was later analyzed using visual and computer-based methods. Capsule load and strain at the time of onset were recorded and compared between the muscle groups. Results indicated capsule load was a better indicator of the tensile stretch thresholds for muscular recruitment than capsule strain. MF responded at significantly smaller capsule loads than TR and LC, while TR and LC activation loads were not significantly different. SM did not respond to physiologic FJC stretch. Muscle group recruitment order reflected the muscles’ fiber type compositions and functional roles in the spine. This study provides the first evidence that the cervical ligamento-muscular reflex pathways are activated via tensile FJC stretch and extend to superficial and deep musculature on the anterior and posterior aspects of the neck, ipsilateral and contralateral to the side of FJC stretch.     

Strain measurement in biaxially loaded inhomogeneous, anisotropic elastic membranes

 This paper considers the problem of measuring the strain field in biaxially loaded elastic membranes, such as soft biological tissue. Cross-correlation of intrinsic or applied speckle patterns were used to calculate the 2D displacements of small regions on the surface of a deforming membrane. This method was able to resolve 2D displacements to within a twentieth of a pixel. A finite-element model with bicubic-Hermite interpolation was used to represent the geometry of the membrane in the undeformed state. This model was fitted to the measured displacements to obtain the geometry of the membrane in the deformed state, and the strain field was calculated from the change in geometry. The strain fields were measured in both an inhomogeneous isotropic rubber membrane and a section of sheep diaphragm. Received: 15 March 2002 / Accepted: 18 August 2002 We would like to acknowledge several people who contributed to the early stages of this project: Marjolein van der Glas and Henri Brouers from the University of Eindhoven contributed while on student exchange visits to Auckland and Peter Apperley helped with instrumentation development for his Masters thesis on biaxial testing. We are also grateful to the reviewers for their extremely useful suggestions. We also gratefully acknowledge the support given by the New Zealand New Economy Research Fund (NERF contract number: UOAX9905).     

Distance dependent centroid to centroid force fields using high resolution decoys

Simplified force fields play an important role in protein structure prediction and de novo protein design by requiring less computational effort than detailed atomistic potentials. A side chain centroid based, distance dependent pairwise interaction potential has been developed. A linear programming based formulation was used in which non-native "decoy" conformers are forced to take a higher energy compared with the corresponding native structure. This model was trained on an enhanced and diverse protein set. High quality decoy structures were generated for approximately 1400 nonhomologous proteins using torsion angle dynamics along with restricted variations of the hydrophobic cores of the native structure. The resulting decoy set was used to train the model yielding two different side chain centroid based force fields that differ in the way distance dependence has been used to calculate energy parameters. These force fields were tested on an independent set of 148 test proteins with 500 decoy structures for each protein. The side chain centroid force fields were successful in correctly identifying approximately 86% native structures. The Z-scores produced by the proposed centroid-centroid distance dependent force fields improved compared with other distance dependent C(alpha)-C(alpha) or side chain based force fields.     

Fluid movement and joint capsule strains due to flexion in rabbit knees

Diarthrodial joints are freely moveable joints containing synovial fluid (SF) within a connective tissue joint capsule that allows for low-friction and low-wear articulation of the cartilaginous ends of long bones. Biomechanical cues from joint articulation regulate synoviocyte and cartilage biology via joint capsule strain, in turn altering the composition of SF. Joint flexion is clinically associated with pain in knees with arthritis and effusion, with the nociception possibly originating from joint capsule strain. The hypothesis of this study was that knee fluid volume distribution and joint capsule strain are altered with passive flexion in the rabbit model. The aims were to (a) determine the volume distribution of fluid in the joint at different total volumes and with flexion of rabbit knees ex vivo, (b) correlate the volume distribution for the ex vivo model to in vivo data, and (c) determine the strains at different locations in the joint capsule with flexion. During knee flexion, ～20% of anteriorly located joint fluid moved posteriorly, correlating well with the fluid motion observed in in vivo joints. Planar joint capsule principal strains were ～100% (tension) in the proximal-distal direction and ～-40% (shortening) in the circumferential direction, relative to the femur axis and 30° strain state. The joint capsule strains with flexion are consistent with the mechanics of the tendons and ligaments from which the capsule tissue is derived. The movement and mixing of SF volume with flexion determine the mechanical and biological fluid environment within the knee joint. Joint fluid movement and capsular strains affect synovial cell biology and likely modulate trans-synovial transport.     

Finite element modelling of the glenohumeral capsule can help assess the tested region during a clinical exam

The objective of this research was to examine the efficacy of evaluating the region of the glenohumeral capsule being tested by clinical exams for shoulder instability using finite element (FE) models of the glenohumeral joint. Specifically, the regions of high capsule strain produced by glenohumeral joint positions commonly used during a clinical exam were identified. Kinematics that simulated a simple translation test with an anterior load at three external rotation angles were applied to a validated, subject-specific FE model of the glenohumeral joint at 60° of abduction. Maximum principal strains on the glenoid side of the inferior glenohumeral ligament (IGHL) were significantly higher than the maximum principal strains on the humeral side, for all three regions of the IGHL at 30° and 60° of external rotation. These regions of localised strain indicate that these joint positions might be used to test the glenoid side of the IGHL during this clinical exam, but are not useful for assessing the humeral side of the IGHL. The use of FE models will facilitate the search for additional joint positions that isolate high strains to other IGHL regions, including the humeral side of the IGHL.     

Elastic properties and masticatory bone stress in the macaque mandible

One important limitation of mechanical analyses with strain gages is the difficulty in directly estimating patterns of stress or loading in skeletal elements from strain measurements. Because of the inherent anisotropy in cortical bone, orientation of principal strains and stresses do not necessarily coincide, and it has been demonstrated theoretically that such differences may be as great as 45 degrees (Cowin and Hart, 1990). Likewise, relative proportions of stress and strain magnitudes may differ. This investigation measured the elastic properties of a region of cortical bone on both the buccal and lingual surfaces of the lower border of the macaque mandible. The elastic property data was then combined with macaque mandibular strain data from published and a new in vivo strain gage experiment to determine directions and magnitudes of maximum and minimum principal stresses. The goal was to compare the stresses and strains and assess the differences in orientation and relative magnitude between them. The main question was whether these differences might lead to different interpretations of mandibular function. Elastic and shear moduli, and Poisson's ratios were measured using an ultrasonic technique from buccal and lingual cortical surfaces in 12 macaque mandibles. Mandibular strain gage data were taken from a published set of experiments (Hylander, 1979), and from a new experiment in which rosette strain gauges were fixed to the buccal and lingual cortices of the mandibular corpus of an adult female Macaca fascicularis, after which bone strain was recorded during mastication. Averaged elastic properties were combined with strain data to calculate an estimate of stresses in the mandibular corpus. The elastic properties were similar to those of the human mandibular cortex. Near its lower border, the macaque mandible was most stiff in a longitudinal direction, less stiff in an inferosuperior direction, and least stiff in a direction normal to the bone's surface. The lingual aspect of the mandible was slightly stiffer than the buccal aspect. Magnitudes of stresses calculated from average strains ranged from a compressive stress of -16.00 GPa to a tensile stress of 8.84 GPa. The orientation of the principal stresses depended on whether the strain gage site was on the working or balancing side. On the balancing side of the mandibles, maximum principal stresses were oriented nearly perpendicular to the lower border of the mandible. On the working side of the mandibles, the orientation of the maximum principal stresses was more variable than on the balancing side, indicating a larger range of possible mechanisms of loading. Near the lower border of the mandible, differences between the orientation of stresses and strains were 12 degrees or less. Compared to ratios between maximum and minimum strains, ratios between maximum and minimum stresses were more divergent from a ratio of 1.0. Results did not provide any major reinterpretations of mandibular function in macaques, but rather confirmed and extended existing work. The differences between stresses and strains on the balancing side of the mandible generally supported the view that during the power stroke the mandible was bent and slightly twisted both during mastication and transducer biting. The calculated stresses served to de-emphasize the relative importance of torsion. On the working side, the greater range of variability in the stress analysis compared to the strain analysis suggested that a more detailed examination of loadings and stress patterns in each individual experiment would be useful to interpret the results. Torsion was evident on the working side; but in a number of experiments, further information was needed to interpret other superimposed regional loading patterns, which may have included parasagittal bending and reverse parasagittal bending.     

Relationships between landscape patterns and species richness of trees,shrubs and vines in a tropical forest

The present study aims to identify and characterize the relationships among landscape structure and plant diversity in a tropical landscape forest in Quintana Roo, Mexico. Total species richness as well as that of trees, shrubs and vines species were identified from 141 sampling quadrats (16,543 individuals sampled). Based on vegetation classes obtained from multi-spectral satellite image classification, I constructed plant diversity maps of the landscape under study using stratified kriging. I calculated the mean number of species in individual patches as the average values of kriging estimates inside of each patch. I then explored the relationships between landscape pattern metrics and the species richness of trees, shrubs and vines, as well as all groups combined using regression analysis. I employed Akaike Information Criterion (AIC) to select a set of candidate models. Based on akaike weights, I calculated model-averaged parameters. Results show that plant diversity of the patches depends on both the quality of the surrounding habitats and the proximity of surrounding patches (i.e., patch isolation).     

Optomotor control of the force of flight in Drosophila and Musca

Specialized networks of movement detectors in the antero-inferior field of the eyes of the fruitfly, Drosophila melanogaster, and the housefly, Musca domestica, respond to upward (or downward) drift of the retinal images by excitation (or inhibition) of the lift-generating force of flight. The influence of the direction of pattern movement upon the altitude control response has been investigated under conditions of fixed flight in still air. Matched model analysis of the available response curves suggests the predominance of unidirectional movement detectors in these networks. Homologous wingbeat-inhibiting detectors in the specified fields of the eyes of the two species respond preferentially to pattern movement from antero-superior to postero-inferior. The arrangement of wingbeat-exciting detectors seems to follow different schemes: These detectors respond preferentially to movement from inferior to superior in Drosophila, and to movement from antero-inferior to postero-superior in Musca. The wingbeat-exciting network in Musca is restricted to a comparatively small antero-equatorial area of the specified fields of the eyes. The combination of the two types of detectors in this area establishes a powerful lift control system which is particularly sensitive to minute deviations from a given level of flight.     

Outermost-cell-surface changes in an encapsulated strain of Staphylococcus aureus after preservation by freeze-drying.

The effects of drying time during freeze-drying on the outermost cell surface of an encapsulated strain of Staphylococcus aureus S-7 (Smith, diffuse) were investigated, with special attention paid to capsule and slime production. To quantify capsule and slime production, capsule antigen production and cellular characteristics such as growth type in serum-soft agar, cell volume index, and clumping factor reaction were examined. After freeze-drying the colonial morphology of strain S-7 was altered from a diffuse to a compact type in serum-soft agar. In accordance with these changes, the titer of the clumping factor reaction increased while the cell volume index, capsule and slime production, and capsule antigen production were markedly decreased in parallel with the period of freeze-drying. The ability of the strain to adhere to collagen, fibrinogen, and soybean lectin was also compared before and after freeze-drying. Fibrinogen levels slightly increased when 10% skim milk and 2% honey were used as cryoprotective agents and showed a remarkable increase when 0.05 M phosphate buffer was used as a control. Also, the ability of strain S-7 to adhere to soybean lectin declined, whereas no changes were observed for collagen under any conditions. Strain S-7 was phage nontypable before freeze-drying but the number of typable cells increased after freeze-drying; phage-typable cells reacted to phage 52 alone after 5 h of freeze-drying, but additional cells also proved to be phage typable to phage 42E after 10 h. Electron micrographs indicated that strain S-7, an encapsulated strain, was converted to an unencapsulated state after freeze-drying.(ABSTRACT TRUNCATED AT 250 WORDS)     

Outermost-cell-surface changes in an encapsulated strain of Staphylococcus aureus after preservation by freeze-drying

The effects of drying time during freeze-drying on the outermost cell surface of an encapsulated strain of Staphylococcus aureus S-7 (Smith, diffuse) were investigated, with special attention paid to capsule and slime production. To quantify capsule and slime production, capsule antigen production and cellular characteristics such as growth type in serum-soft agar, cell volume index, and clumping factor reaction were examined. After freeze-drying the colonial morphology of strain S-7 was altered from a diffuse to a compact type in serum-soft agar. In accordance with these changes, the titer of the clumping factor reaction increased while the cell volume index, capsule and slime production, and capsule antigen production were markedly decreased in parallel with the period of freeze-drying. The ability of the strain to adhere to collagen, fibrinogen, and soybean lectin was also compared before and after freeze-drying. Fibrinogen levels slightly increased when 10% skim milk and 2% honey were used as cryoprotective agents and showed a remarkable increase when 0.05 M phosphate buffer was used as a control. Also, the ability of strain S-7 to adhere to soybean lectin declined, whereas no changes were observed for collagen under any conditions. Strain S-7 was phage nontypable before freeze-drying but the number of typable cells increased after freeze-drying; phage-typable cells reacted to phage 52 alone after 5 h of freeze-drying, but additional cells also proved to be phage typable to phage 42E after 10 h. Electron micrographs indicated that strain S-7, an encapsulated strain, was converted to an unencapsulated state after freeze-drying.(ABSTRACT TRUNCATED AT 250 WORDS)     

Collagen fiber alignment and maximum principal strain in the glenohumeral capsule predict location of failure during uniaxial extension

The glenohumeral joint is frequently dislocated resulting in injury to the glenohumeral capsule. Repair techniques that focus on restoring the capsule after dislocation to re-establish its stabilizing function could benefit from predictions of the location of failure in this continuous sheet of tissue with a random collagen fiber alignment in the unloaded state. Therefore, the objective of this study was to determine the collagen fiber alignment and maximum principal strain in all regions of the capsule during uniaxial extension to failure and to determine whether these parameters could predict the location of tissue failure. Collagen fiber alignment, quantified using a small-angle light-scattering device, and maximum principal strain in the capsule were determined at 5 % increments of elongation until tissue failure. A contingency table analyzed with Fischer’s exact test demonstrated that peak collagen fiber alignment, represented by the normalized orientation index ( $p < 0.001$ ) and maximum principal strain ( $p < 0.001$ ), is significant in predicting location of failure. The direct correlation between the maximum principal strain and collagen fiber alignment measured prior to failure to the location of tissue failure suggests these parameters can be used as a predictive tool to help locate the areas of the glenohumeral capsule that are susceptible to failure. In the future, changes in collagen fiber alignment following injury could be used to develop a constitutive model for injured capsular tissue.     

大兴安岭塔河地区林火发生的优势预测模型选择

选取在经济学和社会科学领域广泛应用的零膨胀模型(zero-inflated models)和栅栏模型(Hurdle models)对大兴安岭地区林火发生进行模拟,应用赤池准则(AIC)、似然比检验(LR)和模型残差平方和(SSR)对两类共4个回归模型——零膨胀泊松模型(ZIP)、零膨胀负二项模型(ZINB)、栅栏泊松模型(PH)、栅栏负二项模型(NBH)进行拟合分析,最终选取适合此林火发生特性的预测模型.模型的AIC和SSR值表明,ZINB模型对当地林火数据的拟合度最高.运用LR检验对嵌套模型(ZINB与ZIP,NBH与PH)进行检验,结果显示: ZINB和NBH均优于各自的嵌入模型,说明负二项(NB)模型对数据结构中的过度离散现象可以很好地模拟和解释.根据研究区林火实际发生规律和两类不同模型的应用假设条件判断,零膨胀模型更适合塔河地区的林火特性.     

Role of the capsule produced by Bacillus megaterium ATCC 19213 in the accumulation of metallic cations

A study was undertaken to determine if the capsule produced by Bacillus megaterium ATCC 19213 was capable of binding metallic ions. For non-toxic metallic ions, this was accomplished by determining the relative concentrations of Fe2+, Ca2+, Zn2+, Mg2+, and Mn2+ removed from a chemically defined medium by the normally capsulated parent strain and two mutants with much smaller capsules. For toxic metals, the rates of respiration of the parent strain and a small capsule mutant in the presence of Cu2+, Hg2+, and Ag1+ were compared. It was found that the parent strain accumulated more Ca2+, Mg2+, and Mn2+. Accumulation of Fe2+ and Zn2+ was similar for the parent strain and the small capsule mutants. Respiration of the parent strain was less inhibited by Cu2+, Hg2+, and Ag1+, indicating that these metals are also bound to the capsule.     

5-氨基-4-氨甲酰咪唑核苷产生菌AIC-90菌种选育研究

已肌苷产生菌枯草杆菌GMI- 741(Ade - )为出发菌株 ,通过多因子诱变选育出具有非精确嘌呤缺陷型、丧失腺嘌呤脱氨酶的AICAR(5 -氨基 - 4-氨甲酰咪唑核苷 )产生菌AIC - 90 ,该菌株摇瓶发酵 72h产AICAR可达 2 0 .3g/L以上。     

Biomechanical response of human spleen in tensile loading

Blunt splenic injuries are most frequently caused as a result of motor vehicle collisions and are associated with high mortality rates. In order to accurately assess the risk of automotive related spleen injuries using tools such as finite element models, tissue level tolerance values and suitable material models must be developed and validated based on appropriate biomechanical data. This study presents a total of 41 tension tests performed on spleen parenchyma coupons and 29 tension tests performed on spleen capsule/parenchyma coupons. Standard dog-bone coupons were obtained from fresh human spleen and tested within 48 h of death. Each coupon was tested once to failure at one of the four loading rates to investigate the effects of rate dependence. Load and acceleration data were obtained at each of the specimen grips. High-speed video and optical markers placed on the specimens were used to measure local displacement. Failure stress and strain were calculated at the location of failure in the gage length of the coupon. The results of the study showed that both the spleen parenchyma and the capsule are rate dependent, with higher loading rates yielding higher failure stresses and lower failure strains. The results also show that the failure stress of the splenic capsule is significantly greater than that of the underlying parenchyma. Overall, this study provides novel biomechanical data that demonstrate the rate dependent tissue level tolerance values of human spleen tissue in tensile loading, which can aid in the improvement of finite element models used to assess injury risk in blunt trauma.     

应用多模型推论估算北部湾多齿蛇鲻的生长参数

生长参数是渔业资源评估和管理策略中的关键参数,因而对目标鱼种选择合适的生长模型至关重要.本文以北部湾多齿蛇鲻为例,采用2006年12月至2009年7逐月采集的体长与年龄鉴定数据(n=2046),运用5个候选生长模型,利用最大似然法在加性误差条件下估算生长参数,并通过模型近似解释率(R²_adj)、根平均方差(RMSE)、赤井信息准则(AIC)和贝叶斯信息准则(BIC)检验模型拟合度.结果表明: 在当前大样本的情况下,4种统计方法在模型拟合度排序上表现一致;多模型推论检验结果表明,Generalized VBGF获得足够的模型支持,并占到AIC权重的95.9%,可以独立描述多齿蛇鲻的体长与年龄的生长关系,生长方程为:L_t=578.49^{\[1-e-0.051(t-0.14)\]0.361.}