An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data

A novel integrative approach has been developed by Lieb and colleagues for analyzing genome-wide datasets of different chromatin-binding factors and epigenetic states that exhibit both sharp and diffuse signals on the genome.     

抗中性粒细胞胞浆抗体、抗核抗体联合检测对类风湿关节炎的诊断价值

目的：探讨抗中性粒细胞胞浆抗体（ANCA）与抗核抗体（ANA）联合检测对类风湿关节炎的临床意义。方法：采用IIF法对82例RA患者（RA组）、74例非RA自身免疫疾病患者（非RA组）和52例健康体检者（正常对照组）的血清ANCA和ANA谱进行了检测分析,并用ELISA法进行抗丝氨酸蛋白酶3（PR3）、抗髓过氧化物酶（MPO）、ANA谱的定量检测。结果：RA组82例患者中,64例ANCA阳性,阳性率为78．08％,其中核周型（PANCA）37例,阳性率为45．1％,胞浆型（CANCA）27例,阳性率为32．9％;非RA组74例患者中有7例ANCA阳性率分别为9．4％;正常对照组50例中没有一例ANCA阳性。利用Elisa法对患者血清进行检测,分别能够特异的检测到PR3、MPO、抗双链DNA抗体（抗ds—DNA抗体）、抗SS—A等抗体、抗ss—A抗体、抗PM—SCL抗体的存在。结论：联合ANCA、ANA检测有助于提高类风湿关节炎的诊断。     

两种联合切口手术治疗眶-上颌-颧骨复合体骨折的对比研究

目的：对比研究冠状-睑下缘-口内联合切口手术与冠状切口联合口腔前庭沟切口手术治疗眶-上颌-颧骨复合体骨折的治疗效果。方法：选取2006年10月-2010年12月眶-上颌-颧骨复合体骨折患者136例,69例患者行冠状-睑下缘-口内联合切口手术,67例行冠状切口联合口腔前庭沟切口手术,分别命名为A组和B组,比较两组患者治疗效果,治疗效果用甲级、乙级和丙级表示。结果：A组治疗效果甲级、乙级、丙级分别为65．2％、30．4％、4．4％,B组治疗效果甲级、乙级、丙级分别为46．3％、29．8％、23．9％,A组治疗效果优于B组;A组术后并发症少于B组。结论：冠状-睑下缘-口内联合切口手术比冠状切口联合口腔前庭沟切口手术更好地治疗眶-上颌-颧骨复合体骨折,治疗效果好,并发症少,能更好地实现颧骨复位。     

The politics of recognition in culturally appropriate care

Over the last 20 years, the concept of culturally appropriate health care has been gradually gaining popularity in medicine and public health. In calling for health care that is culturally appropriate, minority groups seek political recognition of often racialized constructions of cultural difference as they intervene in health care planning and organization. Based on interview narratives from people involved in community organizing to establish a federally funded community health center in a mid-size New England city, I chart the emergence of a language of "culturally appropriate health care" in language used to justify the need for a health center. An identity model of recognition underlies the call for ethnic resemblance between patient and provider seen in many culturally appropriate care programs. I contrast this model of health care with earlier calls for community access and control by activists in the 1970s and explore the practical and theoretical implications of each approach.     

Life Cycle Inventory Information of the United States Electricity System (11/17 pp)

Goal and Scope This study estimates the life cycle inventory (LCI) of the electricity system in the United States, including the 10 NERC (North American Electric Reliability Council) regions, Alaska, Hawaii, off-grid non-utility plants and the US average figures. The greenhouse gas emissions associated with the United States electricity system are also estimated. Methods The fuel mix of the electricity system based on year 2000 data is used. The environmental burdens associated with raw material extraction, petroleum oil production and transportation for petroleum oil and natural gas to power plants are adopted from the DEAMTM LCA database. Coal transportation from a mining site to a power plant is specified with the data from the Energy Information Administration (EIA), which includes the mode of transportation as well as the distance traveled. The gate-to-gate environmental burdens associated with generating electricity from a fossil-fired power plant are obtained from the DEAMTM LCA database and the eGRID model developed by the United States Environmental Protection Agency. For nuclear power plants and hydroelectric power plants, the data from the DEAMTM LCA database are used.Results and Discussion Selected environmental profiles of the US electricity system are presented in the paper version, while the on-line version presents the whole LCI data. The overall US electricity system in the year 2000 released about 2,654 Tg CO2 eq. of greenhouse gas emissions based on 100-year global warming potentials with 193 g CO2 eq. MJe–1 as an weighted average emission rate per one MJ electricity generated. Most greenhouse gases are released during combusting fossil fuels, accounting for 78–95% of the total. The greenhouse gas emissions released from coal-fired power plants account for 81% of the total greenhouse gas emissions associated with electricity generation, and natural gas-fired power plants contribute about 16% of the total. The most significant regions for the total greenhouse gas emissions are the SERC (Southeastern Electric Reliability Council) and ECAR (East Central Area Reliability Coordination Agreement) regions, which account for 22% and 21% of the total, respectively. A sensitivity analysis on the generation and consumption based calculations indicates that the environmental profiles of electricity based on consumption are more uncertain than those based on generation unless exchange data from the same year are available because the exchange rates (region to region import and export of electricity) vary significantly from year to year.Conclusions and Outlook Those who are interested in the LCI data of the US electricity system can refer to the on-line version. When the inventory data presented in the on-line version are used in a life cycle assessment study, the distribution and transmission losses should be taken into account, which is about 9.5% of the net generation [1]. The comprehensive technical information presented in this study can be used in estimating the environmental burdens when new information on the regional fuel mix or the upstream processes is available. The exchange rates presented in this study also offer useful information in consequential LCI studies.     

Environmental Assessment of Freight Transportation in the U.S. (11 pp)

Goal, Scope and Background This study provides a life cycle inventory of air emissions (CO2, NOx, PM10, and CO) associated with the transportation of goods by road, rail, and air in the U.S. It includes the manufacturing, use, maintenance, and end-of-life of vehicles, the construction, operation, maintenance, and end-of-life of transportation infrastructure, as well as oil exploration, fuel refining, and fuel distribution. Methods The comparison is performed using hybrid life cycle assessment (LCA), a combination of process-based LCA and economic input-output analysis-based LCA (EIO-LCA). All these components are added by means of a common functional unit of grams of air pollutant per ton-mile of freight activity. Results and Discussion Results show that the vehicle use phase is responsible for approximately 70% of total emissions of CO2 for all three modes. This confirms that tailpipe emissions underestimate total emissions of freight transportation as infrastructure, pre-combustion, as well as vehicle manufacturing and end-of-life account for a sizeable share of total emissions. Differences between tailpipe emissions and total system wide emissions can range from only 4% for road transportation's CO emissions to an almost ten-fold difference for air transportation's PM10 emissions. Conclusion Rail freight has the lowest associated air emissions, followed by road and air transportation. Depending on the pollutant, rail is 50-94% less polluting than road. Air transportation is rated the least efficient in terms of air emissions, partly due to the fact that it carries low weight cargo. It emits 35 times more CO2 than rail and 18 times more than road transportation on a ton-mile basis. It is important to consider infrastructure, vehicle manufacturing, and pre-combustion processes, whose life-cycle share is likely to increase as new tailpipe emission standards are enforced. Recommendation and Outlook Emission factors, fuel efficiency, and equipment utilization contribute the most to uncertainty in the results. Further studies are necessary to address all variables that influence these parameters, such as road grade, vehicle speed, and vehicle weight. A focus on regional variation, end-of-life processes, fuel refining processes, terminals, as well as more accurate infrastructure allocation between freight and passenger transportation would strengthen the model.     

Urinary biomarkers of 1,3-butadiene in environmental settings using liquid chromatography isotope dilution tandem mass spectrometry

Although, 1,3-butadiene is a known human carcinogen emitted from mobile sources, little is known about traffic-related human exposure to this toxicant. This pilot study was designed to characterize traffic-related environmental exposure to 1,3-butadiene and evaluate its urinary mercapturic acids as biomarkers of exposure in these settings. Personal air samples and multiple urine samples were collected on two separate occasions from three groups of individuals that differed by spatial proximity as well as intensity of traffic: (i) toll collectors, (ii) urban-weekday and (iii) suburban-weekend group. Air samples were analyzed using thermal desorption followed by GC/MS and urine samples were analyzed using isotope dilution liquid chromatography tandem mass spectrometry (ID-LC-MS/MS) for two mercapturic acids of 1,3-butadiene: monohydroxy-3-butenyl mercapturic acid (MHBMA) and 1,2-dihydroxybutyl mercapturic acid (DHBMA). Exposure differed between groups (p<0.05) with median values of 2.38, 1.62 and 0.88 microg/m(3) for toll collectors, the urban-weekday group and the suburban-weekend group, respectively. A refined ID-LC-MS/MS method enabled detection of MHBMA, previously detected only in occupational settings, with high frequency. MHBMA and DHBMA were detected in 95 and 100% of urine samples at levels (mean+/-S.D.) of 9.7+/-9.5, 6.0+/-4.3 and 6.8+/-2.6 ng/mL for MHBMA and 378+/-196, 258+/-133 and 306+/-242 ng/mL for DHBMA for the three different groups, respectively. Mean biomarker levels were higher among the toll collectors compared to the other two groups, however, the differences were not statistically significant (p>0.05). This study is the first to evaluate 1,3-butadiene biomarkers for subtle differences in environmental exposures. However, additional research will be required to ascertain whether the lack of statistical association observed here is real or attributable to unexpectedly small differences in exposure between groups (<1 microg/m(3)), non-specificity of the biomarker at low exposure, and/or small sample size.     

Zeaxanthin Protects Plant Photosynthesis by Modulating Chlorophyll Triplet Yield in Specific Light-harvesting Antenna Subunits

Plants are particularly prone to photo-oxidative damage caused by excess light. Photoprotection is essential for photosynthesis to proceed in oxygenic environments either by scavenging harmful reactive intermediates or preventing their accumulation to avoid photoinhibition. Carotenoids play a key role in protecting photosynthesis from the toxic effect of over-excitation; under excess light conditions, plants accumulate a specific carotenoid, zeaxanthin, that was shown to increase photoprotection. In this work we genetically dissected different components of zeaxanthin-dependent photoprotection. By using time-resolved differential spectroscopy in vivo, we identified a zeaxanthin-dependent optical signal characterized by a red shift in the carotenoid peak of the triplet-minus-singlet spectrum of leaves and pigment-binding proteins. By fractionating thylakoids into their component pigment binding complexes, the signal was found to originate from the monomeric Lhcb4–6 antenna components of Photosystem II and the Lhca1–4 subunits of Photosystem I. By analyzing mutants based on their sensitivity to excess light, the red-shifted triplet-minus-singlet signal was tightly correlated with photoprotection in the chloroplasts, suggesting the signal implies an increased efficiency of zeaxanthin in controlling chlorophyll triplet formation. Fluorescence-detected magnetic resonance analysis showed a decrease in the amplitude of signals assigned to chlorophyll triplets belonging to the monomeric antenna complexes of Photosystem II upon zeaxanthin binding; however, the amplitude of carotenoid triplet signal does not increase correspondingly. Results show that the high light-induced binding of zeaxanthin to specific proteins plays a major role in enhancing photoprotection by modulating the yield of potentially dangerous chlorophyll-excited states in vivo and preventing the production of singlet oxygen.     

Association of the ACE-II genotype with the risk of nephrotic syndrome in Pakistani children

Nephrotic syndrome is a common pediatric glomerular disease associated with heavy proteinuria. Since, the angiotensin converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism is a putative genetic risk factor for NS, in this study, ACE (I/D) polymorphism was analyzed in 268 NS and 223 control samples by a PCR-based method. The genotypic and allelic frequencies were determined and the association between ACE I/D polymorphism and NS was evaluated. The frequency distribution of the II, ID and DD genotypes was 82 (30.6%), 128 (47.8%) and 58 (21.6%) in the NS patients and 9 (4.0%), 171 (76.7%) and 43 (19.3%) in the control samples respectively. In the Pakistani pediatric NS population, the II genotypic and allelic frequencies were found to be significantly associated with the disease (OR = 6.755; C.I = 3-14.9). No significant association was found between this polymorphism and the response to standard steroid therapy. Thus, in contrast to reports from other parts of the world, the II genotype was found to be significantly associated with NS in the Indian and Malay populations and in the Pakistani population described here. To our knowledge, this is the first report from Pakistan describing the association of the ACE I/D polymorphism with pediatric NS. On the basis of these results, it is suggested that analysis of the ACE (I/D) polymorphism should be performed for the early diagnosis in the high risk NS patients in South Asia.     

Phylogenetic reconsideration of Myrmekiaphila systematics with a description of the new trapdoor spider species Myrmekiaphila tigris (Araneae, Mygalomorphae, Cyrtaucheniidae, Euctenizinae) from Auburn, Alabama

The trapdoor spider genus Myrmekiaphila currently comprises 11 nominal species. A recent molecular phylogenetic evaluation of the group identified a number of problems with respect to how species and species groups were delineated by Bond and Platnick in their 2007 taxonomic revision of the genus. We report herein the discovery of a new species, Myrmekiaphila tigrissp. n. The phylogenetic position of the species is evaluated using a molecular phylogenetic approach based on a set of mtDNA markers. Our preferred phylogenetic hypothesis supports the recognition of a new species and further highlights the need to more carefully investigate species boundaries within the genus. These results further indicate that palpal bulb morphology is rapidly evolving and has likely been a contributing factor in rendering a number of species paraphyletic with respect to the molecular data.