Boring's formulation: a scheme for identifying functional neuron groups in a sensory system

In 1935 Edwin Boring proposed that each attribute of sensation reflects the activity of a different neural circuit. If this idea is valid, it could facilitate both psychophysical and neurophysiological research on sensory systems. We think it likely that Boring's formulation is correct for three reasons: 1) Different sensory attributes reflect conscious information about different parameters of a stimulus. To be measured by any device, each of these parameters must be individually computed. Different neural circuits would appear to be necessary for the nervous system to carry out these different computations. 2) Perceived information about different sensory attributes can be made to diverge by appropriate manipulations of the stimuli. If there is a rigorous relationship between conscious sensory experience and neural activity, such a divergence implies that different sensory attributes are served by different neural circuits. 3) Accurate information about a sensory attribute requires that a human observer's attention be focused on that attribute. Changes in direction of attention are thought to involve a process of switching from one neural circuit to another, and provide another way to cause perceived information about different sensory attributes to diverge.     

Understanding beef-cattle farming management strategies by identifying motivations behind farmers' priorities

This study aimed to identify and better understand management strategies that help livestock farmers adapt to changes in their production contexts, a fundamental challenge. A total of nine beef-cattle farmers were interviewed three times over 1 year to discuss 13 dimensions of livestock farming (e.g. reproduction, feeding, sales, etc.). Characterisation of management strategies rested on three main factors: (i) ranking of the dimensions according to the degree to which farmers desired to control them, (ii) reasons for the ranking and (iii) management guidelines. Although farmers agreed upon the rank of certain dimensions, such as herd management, they differed on that of others, such as sales and administration/regulations. Four motivation categories were identified: risk, pleasure, efficiency and ability to control the dimension. Three management guidelines were identified, which indicated that farmers managed for future survival of their farms at different scales (animal/herd v. whole-farm), involving different resources (biological v. financial) and based on different animal categories (reproductive cows v. animals sold). These results improve understanding of individual livestock farmers and their current management strategies by integrating the motivations behind their strategies. For this reason, they constitute methodological elements that agricultural advisors can use to provide relevant information to farmers while accommodating differences in farm management.     

Evaluation of a biochemical test scheme for identifying clinical isolates of Enterococcus faecalis and Enterococcus faecium

AIMS: To evaluate the full test scheme of Facklam and Sahm (1995) for the identification of clinical enterococcal isolates to genus and species level. METHODS AND RESULTS: Fifty-nine clinical isolates, previously provisionally classed as enterococci on the basis of just four biochemical tests of Facklam and Sahm and one other test, were subjected to genus and species identification using the full identification scheme of Facklam and Sahm; 98% of these strains were confirmed to be enterococci and of these, 69% were identified as Enterococcus faecalis and 31% as Enterococcus faecium. Six tests in the scheme (out of 24) gave anomalous or unreliable results for some strains, and two gave unexpected results for the majority of strains presumptively identified as Ent. faecium. CONCLUSIONS: Nine (out of 12) genus tests and nine (out of 12) species tests from the Facklam and Sahm scheme were reliable. Testing for the presence of the Lancefield antigen D was also useful. The majority of presumptive Ent. faecium strains gave different results for the sorbitol and raffinose tests from that expected. SIGNIFICANCE AND IMPACT OF THE STUDY: This study indicates the level of reliability for each of the tests in a current enterococcal identification scheme for differentiating clinical isolates, and showed that two tests gave consistently different test results from those expected for Ent. faecium.     

A data-mining scheme for identifying peptide structural motifs responsible for different MS/MS fragmentation intensity patterns

Although tandem mass spectrometry (MS/MS) has become an integral part of proteomics, intensity patterns in MS/MS spectra are rarely weighted heavily in most widely used algorithms because they are not yet fully understood. Here a knowledge mining approach is demonstrated to discover fragmentation intensity patterns and elucidate the chemical factors behind such patterns. Fragmentation intensity information from 28 330 ion trap peptide MS/MS spectra of different charge states and sequences went through unsupervised clustering using a penalized K-means algorithm. Without any prior chemistry assumptions, four clusters with distinctive fragmentation patterns were obtained. A decision tree was generated to investigate peptide sequence motif and charge state status that caused these fragmentation patterns. This data-mining scheme is generally applicable for any large data sets. It bypasses the common prior knowledge constraints and reports on the overall peptide fragmentation behavior. It improves the understanding of gas-phase peptide dissociation and provides a foundation for new or improved protein identification algorithms.     

Antibiotic resistance of shigellae and rationale for etiotropic therapy of Shigella infections

The study was aimed at determining sensitivity of shigellae to antibacterial preparations and their clinical effectiveness for correcting recommendations on the empirical therapy of acute Shigella infections (ASI). The sensitivity of 164 S. flexneri strains and 80 S. sonnei strains, isolated in 1996-2003 in the Sumy region, Ukraine, was determined with respect to 19 antibacterial preparations: ampicillin (Am), tetracycline (Te), rifampicin (Ri), chloramphenicol (Ca), streptomycin (St), fusidin (Fu), kanamycin (Kn), erythromycin (Er), carbenicillin (Cb), doxycycline (Do), gentamicin (Ge), ofloxacin (Of), cefazolin (Cf), ciprofloxacin (Cp). S. flexneri and S. sonnei were found to be highly sensitive to Am (100%), Te (100%), Cb (90% and 50% respectively), Do (90% and 35% respectively), Fu (100%), Er (100%), Ri (100%), Ca (71.8% and 45% respectively), St (81% and 40% respectively). Some isolated cultures were resistant to fluorochinolones. In addition, the clinical and laboratory analysis of the effectiveness of some preparations was carried out. A total of 202 patients, divided into 6 groups, received furazolidone, chloramphenicol, norfloxacin, phthalazole, polymyxin and the combination of several antibacterial preparations. High efficiency of norfloxacin in the treatment of ASI was confirmed. The use of other preparations and their combinations was found to produce only a slight effect.     

Dams, ducks and DNA: identifying the effects of a hydro-electric scheme on New Zealand's endangered blue duck

Blue duck are conspicuous inhabitants of headwatersections of many rivers in the central North Island of NewZealand. These rivers are also home to a number ofhydro-electricity dams. One scheme in particular – the TongariroPower Development (TPD) involves the reduction and diversion ofwater flow from the headwaters of the Whakapapa, Whanganui andTongariro Rivers in the central North Island of New Zealand. Numbers of the endangered blue duck (Hymenolaimus malacorhynchos)on the Tongariro River have declined markedly in the last decade. Opinions have differed as to whether this indicated a reductionin the `health' of the population or simply a reduction in thecarrying capacity of the river. The issue centered aroundwhether the Tongariro River population was still self-sustaining,or reliant upon immigration from other source rivers. DNAmarkers were used to estimate the relative contributions tooverall recruitment of production from within the population andmigration from external sources. Up to 11 birds were collectedfrom one unmodified population, two stable modified populationsand one declining population. DNA fingerprinting results from twomultilocus probes were analysed using a one-way ANOVA and showedthat mean bandsharing among individuals from the Tongariro River(0.19) was significantly lower than values recorded from thethree other rivers (0.37–0.39). Discovery curves alsoindicated that the Tongariro population contains more geneticvariation than the other three. These results suggest that theTongariro River population is a `sink' dependent upon immigrationfrom a number of different source populations, rather than localproduction.     

A technique for identifying atoms from a screen image

Improving the interfaces in molecular graphics applications, making them more natural and easy to use, is an important task, given the current complexity of the displayed objects and of modeling operations. Clicking near an atom center is the usual method of atom selection. However, this method has certain disadvantages when working with images composed of different atomic representations such as sticks, CPK, or dotted surfaces. We propose another technique allowing the user to obtain the correct answer when he or she clicks on any element of the atom image.     

An induction gene trap for identifying a homeoprotein-regulated locus

An important issue in developmental biology is the identification of homeoprotein target genes. We have developed a strategy based on the internalization and nuclear addressing of exogenous homeodomains, using an engrailed homeodomain (EnHD) to screen an embryonic stem (ES) cell gene trap library. Eight integrated gene trap loci responded to EnHD. One is within the bullous pemphigoid antigen 1 (BPAG1) locus, in a region that interrupts two neural isoforms. By combining in vivo electroporation with organotypic cultures, we show that an already identified BPAG1 enhancer/promoter is differentially regulated by homeoproteins Hoxc-8 and Engrailed in the embryonic spinal cord and mesencephalon. This strategy can therefore be used for identifying and mutating homeoprotein targets. Because homeodomain third helices can internalize proteins, peptides, phosphopeptides, and antisense oligonucleotides, this strategy should be applicable to other intracellular targets for characterizing genetic networks involved in a large number of physiopathological states.     

Safety and immunologic effectiveness of polyantigen from shigellae for oral immunization of monkeys]

Clinical, morphological, and immunological study was carried out in monkeys given shigellae antigen in tablets orally. Each tablet contained 0.5 mg of the antigens obtained by Boiven's method from Sh. flexneri 2a, 3, 4a, 4b, 6 and Sh. sonnei. Daily administration of the preparation for 4 days and then 4 times at the interval of 5 days proved to be harmless for monkeys. A marked immunomorphological reaction in the form of hyperplasia of the lymphoid elements of the wall of the large intestine and the lymph nodes occurred in response. There was found a resistance of the great majority of the immunized animals to the infection with the virulent Sh. flexneri 2a strain, this corresponding to the accumulation of cells secreting IgM and IgA in the wall of the large intestine.     

PHYPred:a tool for identifying bacteriophage enzymes and hydrolases

Dear Editor,Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle.Many studies have reported that phages are more specific to bacteria than antibiotics are;thus,phage therapy has many potential applications in human medicine,with the advantage of having few side effects(Keen,2012).Investigating the mechanisms of bacteria-killing phages will therefore aid