Miracle-dz/UniFAR-FTUs huggingface dataset:
The social structure of the hazel dormouse (Muscardinus avellanarius)

The maintenance of genetic variation is a general conservation concern for endangered species, such as the British hazel dormouse (Muscardinus avellanarius). The structuring of genetic variation at multiple hierarchical levels, from individual through to the total population, can provide insights into within-population processes, such as inbreeding and social behaviour, and help understand the causes of population partitioning, both current and historical. Investigating the processes that shape and alter levels of genetic variation within hazel dormouse populations will highlight any factors that may influence their continued persistence and inform on appropriate management strategies. The current thesis aimed to address whether a) microbial-mediated odour could be a mechanism for kin discrimination, inbreeding avoidance and social cooperation; b) the hazel dormouse displays social structuring and, as a result, evidence for inbreeding avoidance; c) there is within and among population structuring, resulting from identified physical features that restrict gene flow and d) current patterns of genetic variation inform us about historic dispersal. Captive bred individuals of known pedigree were used to assess the relationship between bacterial community composition and relatedness. Microsatellite markers were used to generate relatedness estimates and analyse levels of genetic variation at the individual, social group and sub-population levels on samples obtained from Sussex and the Isle of Wight. Mitochondrial markers were used to infer patterns of genetic variation at the total population level, including samples obtained from all over the species range. F-statistics were then used to infer any deviations from Hardy-Weinberg equilibrium that could imply for example inbreeding or gene flow. The main findings of the thesis are that 1) microbial composition correlates with genetic relatedness in the hazel dormouse, indicating that microbial-mediated odour could be a mechanism for kin discrimination; 2) inbreeding levels are not significantly high, even though both male and female close relatives are in close proximity, with neither sex exclusively practising natal philopatry or dispersal; 3) no identified habitat features appeared to influence gene flow and levels of genetic variation did not differ between sites, regardless of the habitat features; 4) on the basis of mtDNA, the British
Catabolite repression of the Bacillus subtilis hut operon requires a cis-acting site located downstream of the transcription initiation site

Expression of the Bacillus subtilis hut operon is subject to regulation by catabolite repression. A set of hut-lacZ transcriptional fusions was constructed and used to identify two cis-acting sites involved in catabolite repression. The hutOCR1 operator site lies immediately downstream of the hut promoter and weakly regulates hut expression in response to catabolite repression. The downstream hutOCR2 operator site lies within the hutP gene, between positions +203 and +216, and is required for wild-type levels of catabolite repression. Both the hutOCR1 and hutOCR2 operators have sequence similarity to the sites which mediate catabolite repression of several other B. subtilis genes. Two mutations which relieve catabolite repression of hut expression were found to alter the nucleotide sequence of the hutOCR2 operator. Catabolite repression of hut expression was partially relieved in strains containing the ccpA mutation but not in strains containing either the pai or hpr mutation.
Is the SF-12 version 2 Health Survey a valid and equivalent substitute for the SF-36 version 2 Health Survey for the Chinese?

RATIONALE AND OBJECTIVES The scoring algorithm of the 12-item Short-Form Health Survey (SF-12) was revised in the second version (SF-12v2), but information on its psychometric properties is lacking. This study determined whether the SF-12v2 was a valid and equivalent substitute for the SF-36v2 Health Survey (version 2) for the Chinese. METHODS A total of 2410 Chinese adults in Hong Kong completed the SF-36 Health Survey by telephone. The SF-12v2 data were extracted from the SF-36 data. Internal consistency was assessed by Cronbach's alpha, and test-retest reliabilities were evaluated by intraclass correlation. Criterion validity and equivalence were assessed using the SF-36v2 scores as a gold standard. Construct validity and sensitivity were assessed by known-group comparison. RESULTS Internal consistency and test-retest reliabilities were good (range 0.67-0.82) for all except three scales. The SF-12v2 summary scores explained >80% of the total variances of the SF-36v2 summary scores. Construct validity and sensitivity were confirmed by significantly lower SF-12v2 scores in people with chronic diseases than those without. Effect size differences were less than 0.3 and relative validities were greater than 0.7 between SF-12v2 and SF-36v2 scores for different groups. CONCLUSION The SF-12v2 was valid, reliable and sensitive for the Chinese. It is an equivalent substitute for the SF-36v2 for the summary scales.
Identification of Genes Involved in the Acetamidino Group Modification of the Flagellin N-Linked Glycan of Methanococcus maripaludis

ABSTRACT N-linked glycosylation of protein is a posttranslational modification found in all three domains of life. The flagellin proteins of the archaeon Methanococcus maripaludis are known to be modified with an N-linked tetrasaccharide consisting of N-acetylgalactosamine (GalNAc), a diacetylated glucuronic acid (GlcNAc3NAc), an acetylated and acetamidino-modified mannuronic acid with a substituted threonine group (ManNAc3NAmA6Thr), and a novel terminal sugar residue [(5S)-2-acetamido-2,4-dideoxy-5-O-methyl-α-l-erythro-hexos-5-ulo-1,5-pyranose]. To identify genes involved in biosynthesis of the component sugars of this glycan, three genes, mmp1081, mmp1082, and mmp1083, were targeted for in-frame deletion, based on their annotation and proximity to glycosyltransferase genes known to be involved in assembly of the glycan. Mutants carrying a deletion in any of these three genes remained flagellated and motile. A strain with a deletion of mmp1081 had lower-molecular-mass flagellins in Western blots. Mass spectrometry of purified flagella revealed a truncated glycan with the terminal sugar absent and the threonine residue and the acetamidino group missing from the third sugar. No glycan modification was seen in either the Δmmp1082 or Δmmp1083 mutant grown in complex Balch III medium. However, a glycan identical to the Δmmp1081 glycan was observed when the Δmmp1082 or Δmmp1083 mutant was grown under ammonia-limited conditions. We hypothesize that MMP1082 generates ammonia and tunnels it through MMP1083 to MMP1081, which acts as the amidotransferase, modifying the third sugar residue of the M. maripaludis glycan with the acetamidino group.
Efficient Algorithms for Analyzing Cascading Failures in a Markovian Dependability Model

We devise efficient algorithms to construct, evaluate, and approximate a Markovian dependability system with cascading failures. The model, which was previously considered by Iyer et al., represents a cascading failure as a tree of components that instantaneously and probabilistically fail. Constructing the Markov chain presents significant computational challenges because it requires generating and evaluating all such possible trees, but the number of trees can grow exponentially in the size of the model. Our new algorithm reduces runtimes by orders of magnitude compared to a previous method devised by Iyer et al. Moreover, we propose some efficient approximations based on the idea of most likely paths to failure to further substantially reduce the computation time by instead constructing a model that uses only a subset of the trees. We also derive two new dependability measures related to the distribution of the size of a cascade. We present numerical results demonstrating the effectiveness of our approaches. For a model of a large cloud-computing system, our approximations reduce computation times by orders of magnitude with only a few percent error in the computed dependability measures.
The Helsinki Declaration on Patient Safety in Anaesthesiology

Anaesthesiology, which includes anaesthesia, perioperative care, intensive care medicine, pain therapy and emergency medicine, has always participated in systematic attempts to improve patient safety. Anaesthesiologists have a unique, cross-specialty opportunity to influence the safety and quality of patient care. Past achievements have allowed our specialty a perception that it has become safe, but there should be no room for complacency when there is more to be done. Increasingly older and sicker patients, more complex surgical interventions, more pressure on throughput, new drugs and devices and simple chance all pose hazards in the work of anaesthesiologists. In response to this increasingly difficult and complex working environment, the European Board of Anaesthesiology (EBA), in cooperation with the European Society of Anaesthesiology (ESA), has produced a blueprint for patient safety in anaesthesiology. This document, to be known as the Helsinki Declaration on Patient Safety in Anaesthesiology, was endorsed by these two bodies together with the World Health Organization (WHO), the World Federation of Societies of Anaesthesiologists (WFSA), and the European Patients' Federation (EPF) at the Euroanaesthesia meeting in Helsinki in June 2010. The Declaration represents a shared European view of that which is worthy, achievable, and needed to improve patient safety in anaesthesiology in 2010. The Declaration recommends practical steps that all anaesthesiologists who are not already using them can successfully include in their own clinical practice. In parallel, EBA and ESA have launched a joint patient safety task-force in order to put these recommendations into practice. It is planned to review this Declaration document regularly.
Plant growth promoting capability and genetic diversity of bacteria isolated from mud volcano and lime cave of Andaman and Nicobar Islands

Twenty four bacterial strains from four different regions of mud volcano and lime cave were isolated to estimate their diversity, plant growth promoting and biocontrol activities to use them as inoculant strains in the fields. An excellent antagonistic effect against four plant pathogens and plant growth promoting properties such as IAA production, HCN production, phosphate solubilization, siderophore production, starch hydrolysis and hydrolytic enzymes syntheses were identified in OM5 (Pantoea agglomerans) and EM9 (Exiguobacterium sp.) of 24 studied isolates. Seeds (Chili and tomato) inoculation with plant growth promoting strains resulted in increased percentage of seedling emergence, root length and plant weight. Results indicated that co-inoculation gave a more pronounced effects on seedling emergence, secondary root numbers, primary root length and stem length, while inoculation by alone isolate showed a lower effect. Our results suggest that the mixed inocula of OM5 and EM9 strains as biofertilizers could significantly increase the production of food crops in Andaman archipelago by means of sustainable and organic agricultural system.
Completion Rate and Side-Effect Profile of Three-Month Isoniazid and Rifapentine Treatment for Latent Tuberculosis Infection in an Urban County Jail

In an urban jail population, 3 months of isoniazid and rifapentine (3HP) was associated with an 85% latent tuberculosis infection treatment completion rate compared with 18% in a standard 9-month isoniazid treatment group. Among the 91 patients who started 3HP therapy, there were 2 treatment discontinuations from adverse drug reactions.
Complementarity Between a Docking and a High-Throughput Screen in Discovering New Cruzain Inhibitors†

Virtual and high-throughput screens (HTS) should have complementary strengths and weaknesses, but studies that prospectively and comprehensively compare them are rare. We undertook a parallel docking and HTS screen of 197861 compounds against cruzain, a thiol protease target for Chagas disease, looking for reversible, competitive inhibitors. On workup, 99% of the hits were eliminated as false positives, yielding 146 well-behaved, competitive ligands. These fell into five chemotypes: two were prioritized by scoring among the top 0.1% of the docking-ranked library, two were prioritized by behavior in the HTS and by clustering, and one chemotype was prioritized by both approaches. Determination of an inhibitor/cruzain crystal structure and comparison of the high-scoring docking hits to experiment illuminated the origins of docking false-negatives and false-positives. Prioritizing molecules that are both predicted by docking and are HTS-active yields well-behaved molecules, relatively unobscured by the false-positives to which both techniques are individually prone.
Human immunodeficiency virus infection in trauma patients: where do we stand?

OBJECTIVE The human immunodeficiency virus (HIV) epidemic is a growing health care problem. The purpose of this study was to examine the relationship between HIV infection and trauma patient treatment, complications, and mortality. METHODS The Pennsylvania Trauma Outcome Study database was used to identify trauma patients with known HIV-positive status (HP) and randomly selected age-matched controls (CL). Demographics, Injury Severity Score, Glasgow Coma Scale score, mechanism of injury, preexisting conditions, complications, mortality, hospital length of stay (HLOS), intensive care unit length of stay (ILOS), and operative interventions were compared. RESULTS Demographics, vital signs on presentation, and Injury Severity Score were similar between the HP and CL groups. There was no difference in mortality between the two groups (3.6% vs. 3.1%, p = 0.6447). HP patients were more likely to present with penetrating injuries (22.6% vs. 15.8%, p < 0.0031) and had significantly fewer major orthopedic injuries than CL patients (p < 0.01). HP patients were more likely to have a history of a neurologic condition; chronic drug/alcohol use; psychiatric diagnosis; or liver, pulmonary, and/or renal disease (all p < 0.01). HP patients had more pulmonary complications (12.3% vs. 4.1%), renal complications, and infectious/septic complications (all p < 0.01) than controls. Infection/sepsis and pulmonary complications were associated with significant mortality in HP patients. HP patients underwent more thoracostomies (7.5% vs. 4.4%, p = 0.0235) and exploratory laparotomies (7.0% vs. 2.4%, p = 0.0002). HLOS (10.2 +/- 10 vs. 6.8 +/- 8.6 days, p = 0.001) and ILOS (2.3 +/- 7.2 vs. 1.5 +/- 4.9 days, p = 0.0178) were greater for HP patients. HP patients were less likely than controls to be discharged directly to home (67.8% vs. 82.7%, p = 0.0001). CONCLUSION HP patients had more preexisting conditions and complications than controls. There was no difference in overall mortality between the two groups. However, pulmonary/infectious complications were associated with significant mortality in HP patients. HP patients consumed more health care resources than controls, as exemplified by greater ILOS and HLOS and more operative procedures.
Performance Analysis for Large IaaS Clouds

IaaS clouds are major enablers of data-intensive cloud applications because they provide necessary computing capacity for managing Big Data environments. In a typical IaaS cloud, virtual machine (VM) instances deployed on physical machines (PM) are provided to the users for their computing needs. Recently, IaaS cloud providers are realizing that merely providing the basic functionalities for Big Data processing is not sufficient to survive intense business competitions. Rather, the performance of the cloud provided service is an equally important factor when a CONTENTS
Leg mechanics contribute to establishing swing phase trajectories during memory-guided stepping movements in walking cats: a computational analysis

When quadrupeds stop walking after stepping over a barrier with their forelegs, the memory of barrier height and location is retained for many minutes. This memory is subsequently used to guide hind leg movements over the barrier when walking is resumed. The upslope of the initial trajectory of hind leg paw movements is strongly dependent on the initial location of the paw relative to the barrier. In this study, we have attempted to determine whether mechanical factors contribute significantly in establishing the slope of the paw trajectories by creating a four-link biomechanical model of a cat hind leg and driving this model with a variety of joint-torque profiles, including average torques for a range of initial paw positions relative to the barrier. Torque profiles for individual steps were determined by an inverse dynamic analysis of leg movements in three normal cats. Our study demonstrates that limb mechanics can contribute to establishing the dependency of trajectory slope on the initial position of the paw relative to the barrier. However, an additional contribution of neuronal motor commands was indicated by the fact that the simulated slopes of paw trajectories were significantly less than the observed slopes. A neuronal contribution to the modification of paw trajectories was also revealed by our observations that both the magnitudes of knee flexor muscle EMG bursts and the initial knee flexion torques depended on initial paw position. Previous studies have shown that a shift in paw position prior to stepping over a barrier changes the paw trajectory to be appropriate for the new paw position. Our data indicate that both mechanical and neuronal factors contribute to this updating process, and that any shift in leg position during the delay period modifies the working memory of barrier location.
Prevalence of Adenomas among Young Individuals at Average Risk for Colorectal Cancer

OBJECTIVES:We evaluated the prevalence and characteristics of adenomas in a young population not genetically predisposed for the development of colorectal cancer (CRC). METHODS:The databases of the Dutch Hereditary Colorectal Cancer Registry were used. The study population included patients (n = 444) who had regular endoscopy until mutation analysis revealed they did not carry the (Adenomatous Polyposis Coli (APC)/Mismatch Repair) gene defect identified in their family.RESULTS:At first colonoscopy (n = 342; 50% males, mean age 37 yr) a total of 19 adenomas (10 males, mean age 50 yr, range 24–91 yr) and two CRCs (2 males, age 49 and 72 yr) were identified, and at first sigmoidoscopy (n = 102; 53% males, mean age 29 yr) three adenomas (2 males, age 8, 40, and 41 yr) were found. A second colonoscopy was performed in 14 patients with, and in 162 patients without an adenoma. Three of 14 patients (21%) developed a new adenoma (all >50 yr) and 8 of 162 (5%) patients developed their first adenoma during follow-up. In the colonoscopy group, the cumulative proportion of patients free of adenomas at age 50 yr was 86%. Of all adenomas diagnosed during colonoscopy (n = 49), 65% were located distal from the flexura lienalis. Of the adenomas detected during all endoscopies (n = 53), 9.8% were ≥7 mm, 7.5% showed high-grade dysplasia, and 7.5% showed tubulovillous features.CONCLUSION:On the basis of our findings during colonoscopy we conclude that the risk of developing adenomas/CRC in young individuals without genetic risk factors is low. Adenoma surveillance programs should focus on young individuals with a positive family (or personal) history for adenomas/CRC, or on individuals >50 yr.
The Hematologic Response to Anti-apoptotic Cytokine Therapy: Results of Pentoxifylline, Ciprofloxacin, and Dexamethasone Treatment for Patients with Myelodysplastic Syndrome

TNF-α mediated apoptosis of the hematopoietic cells has been thought to contribute to the ineffective hematopoiesis observed in myelodysplastic syndrome (MDS). The combination of pentoxifylline (P) and ciprofloxacin (C) has been shown to reduce the serum levels of TNF-α, and an earlier trial of P and C with dexamethasone (D) provided good palliation for patients with MDS. The purpose of this study is to assess the hematologic response to PCD therapy for patients suffering with MDS. 21 of 25 patients who completed at least of 12 weeks of treatment were evaluable for the treatment efficacy. At baseline, the patient's median age was 60 yr (range: 18-75 yr). The diagnoses according to WHO classification included: RA (n=5), RCMD (n=10), RARS (n=1), RCMD/RS (n=1), RAEB (3), and CMML (n=1). 11 patients (52%) had at least single lineage response. 3 patients (11%) showed improvement of triple lineage cytopenia. There were no differences in the response rates between the FAB subtypes. The median time to response was 4 weeks (range: 2-12 weeks), and it is interesting that 9 of 11 patients who had a response remained without relapse for a median of 177 days (range: 78-634 days). These preliminary results indicate that anti-cytokine therapy with PCD is an effective and well tolerated palliative treatment for patients with MDS.
Active tectonics in southern Xinjiang, China: Analysis of terrace riser and normal fault scarp degradation along the Hotan‐Qira Fault System

The northern piedmont of the western Kunlun mountains (Xinjiang, China) is marked at its easternmost extremity, south of the Hotan-Qira oases, by a set of normal faults trending N50E for nearly 70 km. Conspicuous on Landsat and SPOT images, these faults follow the southeastern border of a deep flexural basin and may be related to the subsidence of the Tarim platform loaded by the western Kunlun northward overthrust. The Hotan-Qira normal fault system vertically offsets the piedmont slope by 70 m. Highest fault scarps reach 20 m and often display evidence for recent reactivations about 2 m high. Successive stream entrenchments in uplifted footwalls have formed inset terraces. We have leveled topographic profiles across fault scarps and transverse abandoned terrace risers. The state of degradation of each terrace edge has been characterized by a degradation coefficient τ, derived by comparison with analytical erosion models. Edges of highest abandoned terraces yield a degradation coefficient of 33 ± 4 m^2. Profiles of cumulative fault scarps have been analyzed in a similar way using synthetic profiles generated with a simple incremental fault scarp model. The analysis shows that (1) rate of fault slip remained essentially constant since the aggradation of the piedmont surface and (2) the occurrence of inset terraces was synchronous at all studied sites, suggesting a climate-driven terrace formation. Observation of glacial and periglacial geomorphic features along the northern front of the western Kunlun range indicates that the Qira glaciofluvial fan emplaced after the last glacial maximum, during the retreat of the Kunlun glaciers (12–22 ka). The age of the most developed inset terrace in uplifted valleys is inferred to be 10 ± 3 ka, coeval with humid climate pulses of the last deglaciation. The mass diffusivity constant (k=τ/T, being time B.P.) in the Hotan region is determined to be 3.3 ± 1.4 m^2/10^3 years, consistent with other estimates in similar climatic and geologic environments of western China. These results imply a minimum rate for the Tarim subsidence of 3.5 ± 2 mm/yr. If Western Kunlun overthrusts the Tarim platform on a crustal ramp dipping 40°–45° to the south, it would absorb at least 4.5 ± 3 mm/yr of convergence between western Tibet and Tarim.