Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmid diversity of multi-drug-resistant Escherichia coli isolated from children with diarrhoea in a poultry-farming area in Kenya.

Biotin-labelled DNA probes and restriction-endonuclease digestion (RED) with HindIII were used to study the diversity of resistance plasmids (R-plasmids) from 414 Escherichia coli isolates: 168 from children living in close contact with antibiotic-fed poultry and 246 from the chickens. Full sensitivity to all 10 antimicrobials tested was more common in the isolates from poultry than in those from the children (36.2% v. 9.5%; P < 0.001). Multi-drug resistance, to at least two of the antimicrobials, was relatively common in the isolates from the children (85.5% v. 26.00%; P < 0.001). Overall, 31% of the poultry isolates were resistant to tetracycline alone. Resistance to amoxycillin was due to production of TEM-1 (89%) and TEM-2 (11%). In > 71% of the isolates from children and 79% of those from poultry, resistance was encoded on a 100-110-kb transferable plasmid belonging to incompatibility group FII. However, RED patterns of R-plasmids from the two groups of isolates were highly diverse and not indicative of any close relatedness. This difference in patterns and in the levels of multi-drug resistance indicate that the isolates from the children and those from the poultry represent two distinct pools of resistance plasmids.
A simulation study of the effect of drift electric fields on the response of radiation detectors using the PENELOPE code

The effect of the presence of a drift electric field on the response of gaseous and semiconductor radiation detectors to energetic X-rays (energies Eph from 20 to 200 keV) is investigated using the PENELOPE code to simulate the photo-absorption and the slow-down of the electrons produced in Si, Ge, and Xe gas at 1 atm. For typical drift fields, the energy Ed deposited in the detection media is calculated taking into account the energy exchanged by the electrons with the field. The analysis of the calculated Ed distributions shows that the effect of the field on the distributions is negligible in Si and Ge semiconductor detectors, but not in Xe gas detectors, where for E=p 1⁄4 0:8V cm 1 Torr 1 the fluctuations introduced by the field for Eph 180 keV approach the intrinsic values for Xe, and the intrinsic discontinuity in linearity when Eph crosses the Xe K-edge (34.56 keV) is further reduced by 4%. The simulation data also suggest that this field effect may cause some deviations to the expected Gaussian response of Xe detectors to the absorption of monoenergetic photons. r 2006 Elsevier B.V. All rights reserved. PACS: 29.40. n; 29.40. Cs; 29.40. Wk; 29.30. Kv
Nonsense-mediated mRNA decay at the crossroads of many cellular pathways

Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism ensuring the fast decay of mRNAs harboring a premature termination codon (PTC). As a quality control mechanism, NMD distinguishes PTCs from normal termination codons in order to degrade PTC-carrying mRNAs only. For this, NMD is connected to various other cell processes which regulate or activate it under specific cell conditions or in response to mutations, mis-regulations, stresses, or particular cell programs. These cell processes and their connections with NMD are the focus of this review, which aims both to illustrate the complexity of the NMD mechanism and its regulation and to highlight the cellular consequences of NMD inhibition.
Advancing donor liver age and rapid fibrosis progression following transplantation for hepatitis C

Background and aims: Cirrhosis with liver failure due to hepatitis C virus (HCV) infection is the most common indication for liver transplantation (LT). Reinfection of the transplanted liver by HCV is inevitable, and aggressive hepatitis with accelerated progression to graft cirrhosis may be observed. Of concern, recent reports suggest that the outcome of LT for HCV may have deteriorated in recent years. Determinants of rate of progression to cirrhosis in the immunocompetent non-transplant patient are well defined, and the most powerful determinant is patient age at the time of infection. Following LT for HCV, recipient age does not affect outcome of HCV reinfection. However, the impact of donor age on graft fibrosis progression rate following LT has not been examined. Methods: We have examined post-transplant biopsies to assess histological activity, including fibrosis stage (scored 0–6 units, 6 representing established cirrhosis), and to calculate fibrosis progression rates in 101 post-transplant specimens from 56 HCV infected LT patients. Univariate and multivariate analyses examined the impact of parameters including recipient and donor age and sex on fibrosis progression rate, and on predicted time to cirrhosis. Results: For the cohort, median fibrosis progression rate was 0.78 units/year, and median interval from transplantation to development of cirrhosis was 7.7 years. In multivariate analysis, donor age (not recipient age) was a powerful determinant (p=0.02) of fibrosis progression rate. When the liver donor was younger than 40 years, median progression rate was 0.6 units/year and interval to cirrhosis was 10 years. When the donor was aged 50 years or more, median progression rate was 2.7 units/year and interval to cirrhosis only 2.2 years. During the observation period there has been a significant increase in donor age (p=0.01) but date of transplantation per se is not a determinant of progression rate when included in multivariate analyses. Conclusions: Donor age has a major influence on graft outcome following transplantation for HCV. The changing organ donor profile will affect the long term results of LT for HCV. These observations have important implications for donor liver allocation.
Motor proficiency predicts cognitive ability in four-year-olds

Research has shown links between motor proficiency and cognition in school-age children, however, few have explored earlier ages. We aimed to determine the association between motor proficiency and cognitive ability in four-year-olds. Motor and cognitive skills were examined in 32 (15 males, 17 females) four-year-olds (±5.59 months) using the Bruininks-Oseretsky Test of Motor Proficiency (BOT-2) (Fine Manual Control [FMC], Manual Coordination [MC], Body Coordination [BC], and Strength & Agility [SA]) and the Kaufman Brief Intelligence Test (KBIT-2) (Verbal, Nonverbal, and IQ). Correlation analysis revealed significance between BC and Verbal (.45) and IQ (.51), including MC and IQ (.55). Total Motor Proficiency displayed significance to Verbal (.49), Nonverbal (.40), and IQ (.58). Through regression analysis, MC predicted Verbal (32%) and IQ (31%), while Total Motor Proficiency predicted Verbal (24%), Nonverbal (16%), and IQ (34%). Motor proficiency appears to be associated with cognition, thus emphasizing the importance of early motor skill development.
Maximum likelihood estimation in semiparametric regression models with censored data

Summary. Semiparametric regression models play a central role in formulating the effects of covariates on potentially censored failure times and in the joint modelling of incomplete repeated measures and failure times in longitudinal studies. The presence of infinite dimensional parameters poses considerable theoretical and computational challenges in the statistical analysis of such models. We present several classes of semiparametric regression models, which extend the existing models in important directions. We construct appropriate likelihood functions involving both finite dimensional and infinite dimensional parameters. The maximum likelihood estimators are consistent and asymptotically normal with efficient variances. We develop simple and stable numerical techniques to implement the corresponding inference procedures. Extensive simulation experiments demonstrate that the inferential and computational methods proposed perform well in practical settings. Applications to three medical studies yield important new insights. We conclude that there is no reason, theoretical or numerical, not to use maximum likelihood estimation for semiparametric regression models. We discuss several areas that need further research.
Physical activity participation amongst individuals with lower limb amputation

Abstract Purpose: To examine physical activity participation amongst individuals with lower limb amputation. Method: Adults with lower limb amputation were convenience-sampled from a major metropolitan hospital outpatient amputee service and completed the International Physical Activity Questionnaire. Results: Seventy-two individuals (65% male), mean age 53.6 (SD = 16.8) years, who were 10.8 (SD = 12.6) years post amputation (60% transtibial) participated in the study. Thirty-eight percent of participants (n = 27) undertook “high” levels, 26% (n = 19) undertook “moderate” levels, and 36% (n = 26) undertook “low” levels of physical activity but cumulative activity levels were low. Participants most commonly undertook domestic-related activities (n = 53, 74%) and moderate-intensity activities (n = 54, 75%). Physical activity levels were found to be significantly lower amongst individuals who did not work, individuals with dysvascular amputation and individuals who lived with others. Physical activity levels showed a weak, significant, correlation to age (rs (70) = −0.259, p = 0.028) and time post amputation (rs (70) = 0.237, p = 0.049). Conclusion: This study provides clinicians with information about physical activity participation amongst individuals with lower limb amputation. The majority of participants in this study (n = 44, 61%) did not accumulate sufficient “total physical activity” to be classified as “sufficiently active” and 33% (n = 24) of participants were classified as “sedentary”. Implications for Rehabilitation Regular physical activity participation is associated with many health benefits. This study found the majority of individuals with lower limb amputation (61%) did not undertake sufficient total physical activity to be classified as “sufficiently active”. Health professionals working in rehabilitation can play an important role in encouraging individuals to increase physical activity participation. The study’s findings may guide health professionals on where to direct their focus to promote increased physical activity participation amongst individuals with lower limb amputation.
Cultural scripts for multiple and concurrent partnerships in southern Africa: why HIV prevention needs anthropology.

BACKGROUND Multiple and concurrent sexual partnerships have been identified as southern Africa's key behavioural driver of HIV, resulting in calls to make partner reduction programming central to an intensified HIV prevention focus. Various efforts are currently being made in the region in response to this call. Such efforts will likely have as limited success as past prevention efforts if the cultural milieu in which sexual partnering practices are located and reproduced remains poorly understood, unaccounted for, and unaddressed in prevention programming. METHODS Focussed ethnographic discussions were held between October 2007 and November 2008 with 228 members of southern African non-government organisations representing seven countries. Discussions formed part of follow-up activities to a high level regional meeting and were aimed at exploring contextual factors in HIV transmission, most especially the role of culture in relation to multiple and concurrent partnerships. RESULTS Common patterns in cultural scripts for the performance of sexuality were discernable. Several predominant scripts that tend to affirm and lend cultural legitimacy to multiple and concurrent partnering were identified, discussed and analysed. CONCLUSION Effectuating change at the level of cultural scripting to discourage multiple and concurrent partnerships is required for sustainable long-term protection of people and communities against HIV. The success of partner reduction programs will be largely determined by the extent to which they are informed by anthropological knowledge and work with cultural logics to allow people to envision how they can transform obstacles into support for risk reduction.
Influence of microgravity on astronauts' sympathetic and vagal responses to Valsalva's manoeuvre

When astronauts return to Earth and stand, their heart rates may speed inordinately, their blood pressures may fall, and some may experience frank syncope. We studied brief autonomic and haemodynamic transients provoked by graded Valsalva manoeuvres in astronauts on Earth and in space, and tested the hypothesis that exposure to microgravity impairs sympathetic as well as vagal baroreflex responses. We recorded the electrocardiogram, finger photoplethysmographic arterial pressure, respiration and peroneal nerve muscle sympathetic activity in four healthy male astronauts (aged 38–44 years) before, during and after the 16 day Neurolab space shuttle mission. Astronauts performed two 15 s Valsalva manoeuvres at each pressure, 15 and 30 mmHg, in random order. Although no astronaut experienced presyncope after the mission, microgravity provoked major changes. For example, the average systolic pressure reduction during 30 mmHg straining was 27 mmHg pre‐flight and 49 mmHg in flight. Increases in muscle sympathetic nerve activity during straining were also much greater in space than on Earth. For example, mean normalized sympathetic activity increased 445 % during 30 mmHg straining on earth and 792 % in space. However, sympathetic baroreflex gain, taken as the integrated sympathetic response divided by the maximum diastolic pressure reduction during straining, was the same in space and on Earth. In contrast, vagal baroreflex gain, particularly during arterial pressure reductions, was diminished in space. This and earlier research suggest that exposure of healthy humans to microgravity augments arterial pressure and sympathetic responses to Valsalva straining and differentially reduces vagal, but not sympathetic baroreflex gain.
Selective enhancement of rapid eye movement sleep by deep brain stimulation of the human pons

Animal studies suggest that rapid eye movement (REM) sleep is governed by the interaction of REM‐promoting and REM‐inhibiting nuclei in the pontomesencephalic tegmentum. The pedunculopontine nucleus is proposed to be REM promoting. Using polysomnography, we studied sleep in five parkinsonian patients undergoing unilateral pedunculopontine nucleus deep brain stimulation (DBS). We demonstrated a near doubling of nocturnal REM sleep between the DBS “off” and DBS “on” states, without significant changes in other sleep states. This represents the first demonstration that DBS can selectively modulate human sleep, and it supports an important role for the pedunculopontine nucleus region in modulating human REM sleep. Ann Neurol 2009;66:110–114
Memory system behavior of Java programs: methodology and analysis

This paper studies the memory system behavior of Java programs by analyzing memory reference traces of several SPECjvm98 applications running with a Just-In-Time (JIT) compiler. Trace information is collected by an exception-based tracing tool called JTRACE, without any instrumentation to the Java programs or the JIT compiler. First, we find that the overall cache miss ratio is increased due to garbage collection, which suffers from higher cache misses compared to the application. We also note that going beyond 2-way cache associativity improves the cache miss ratio marginally. Second, we observe that Java programs generate a substantial amount of short-lived objects. However, the size of frequently-referenced long-lived objects is more important to the cache performance, because it tends to determine the application's working set size. Finally, we note that the default heap configuration which starts from a small initial heap size is very inefficient since it invokes a garbage collector frequently. Although the direct costs of garbage collection decrease as we increase the available heap size, there exists an optimal heap size which minimizes the total execution time due to the interaction with the virtual memory performance.
Highly sensitive biosafety model for stem-cell-derived grafts.

BACKGROUND The recent success in the derivation of differentiated cell types from stem cells has raised prospects for the application of regenerative cell therapy. In particular, embryonic stem cells are attractive sources for cell transplantation, due to their immortality and rapid growth. These cells, however, also possess tumorigenic properties, which raises serious safety concerns and makes biosafety testing mandatory. Our goal was to establish a highly sensitive animal model for testing the proliferative potential of stem-cell grafts. METHODS BALB/c nude mice received cell grafts of non-neoplastic MRC-5 cells containing defined numbers of mouse embryonic stem cells. We either injected 1 million viable cells into the kidney capsule, or mixed 2 million cells with Matrigel for s.c. transplantation. To analyze the possible impact of an intact immune response on tumor development, we also transplanted the cells into immunocompetent mice. Animals were sacrificed when the tumors became >1 cm and were analyzed in detail. RESULTS The nude mouse model reproducibly allowed detection of 20 tumorigenic cells, and even as few as 2 ES cells were found to form teratoma. Interestingly, the administration of cell grafts at two different application sites resulted in different growth kinetics and tumor phenotypes. The highest level of sensitivity (100% detection of 20 tumorigenic ES cells) was achieved by s.c. injection of cells mixed with Matrigel. The influence of the immune system on tumor-cell development was demonstrated by a higher tumor rate of transplants in immunodeficient nude mice compared with immunocompetent mice. DISCUSSION We have established a reliable animal model for routine assessment of the biosafety profile of stem-cell-derived cell transplants. This model will facilitate the generation of homogenous non-tumorigenic cell populations, and will help to integrate standardized safety systems into the application of stem-cell-derived grafts for clinical purposes.
[Effects of Radix Astragali on IL-1beta, TNF-alpha and antigen expression of peripheral blood mononuclear cells in patients with Graves disease].

OBJECTIVE To study the effects of Radix Astragali on serum cytokines IL-1beta, TNFalpha and antigen expression of peripheral blood mononuclear cells (PBMCs) in patients with Graves disease (GD). METHODS Eighty GD patients at their first visit were randomly assigned to the methimazole (MMI) group (Group A) and the MMI combined Radix Astragali group (Group B), 40 in each. The improvement of clinical symptoms and thyroid functions were observed after one-month treatment. The serum IL-1beta and TNF-alpha levels in the peripheral blood were determined using radioimmunoassay. The expression levels of surface antigen CD80, CD54, and HLA-DR of PBMCs were detected using flow cytometry. RESULTS The improvement of the thyroid gland function was similar in the two groups. There was no obvious change in the levels of autoantibody TGAb or TPOAb of the two groups. Symptoms such as fear of heat, hidrosis, palpitation, and so on were more obviously improved in Group B than in Group A (P < 0.05). The serum IL-betaP, TNFalphaa, CD00 levels in the peripheral blood were all improved in the two groups after treatment when compared with before treatment ( P < 0.05 or P < 0.01). But the serum levels of IL-beta and TNFalpha decreased more obviously in Group B than in Group A ( P < 0.05). The expression of CD54 decreased more obviously in Group B (P < 0.01), showing statistical difference when compared with Group A at the same time point (P < 0.05). CONCLUSION Radix Astragali could significantly relieve the clinical symptoms such as hidrosis and palpitation, regulate the immune function of GD patients, playing an important role in the adjuvant therapy for GD.
Tension between Local and Global Optimization in the Experiments

Social dilemmas specify situations in which (local) egoistic utility optimization prevents achieving the (global) common good of a group. Tragically, in such dilemmas local optimization also reduces the payoff for the individual optimizer. Although social dilemmas essentially reflect inter-individual contexts (conflicting interests, moral attitudes, etc.), innerindividual dilemmas apparently share at least some structural aspects with them: individual behavior can concern more conflicting levels of optimization. For example, starting additional academic projects with potentially positive ‘payoff’ may assume ‘more is more’. However, exogenous effects may arise from optimizing local goals; further contributions may incrementally reduce the quality of other contributions and yield ‘more is less’. In three experiments we explore a oneperson investment game about building hotels, reflecting a social dilemma. The payoffs involve different optima for local and global optimization. Results show that people can be influenced by a default-strategy of ‘more is more’, even if it is irrational.
Design of an intelligent hospital service robot and its applications

The paper presents the design concepts of an intelligent hospital service robot (IHSR). The IHSR aims at saving human resources and also improving the hospital service. The navigation path planning can be concluded by an information decision making system. It is decided from the distribution of people in the hospital. For obstacle avoidance, the IHSR mounts a CCD camera and its attachments to determine the relative directions of obstacles. There are nine ultrasonic sensors installed on the IHSR to detect the distances between the IHSR and obstacles. An integrated fuzzy controller is proposed as the collision-free navigation control system. In which, there are two fuzzy subcontrollers designed for objective navigation and collision-free control respectively. Simulation results show that the IHSR is indeed able to accomplish navigation control in hospital environment.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

MOTIVATION Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain. Current methods do not fully meet this need because they require a reference, only consider one of the many aspects of assembly quality or lack statistical justification, and none are designed to evaluate metagenome assemblies. RESULTS In this article, we present an Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment and k-mer frequency. ALE pinpoints synthetic errors in both single and metagenomic assemblies, including single-base errors, insertions/deletions, genome rearrangements and chimeric assemblies presented in metagenomes. At the genome level with real-world data, ALE identifies three large misassemblies from the Spirochaeta smaragdinae finished genome, which were all independently validated by Pacific Biosciences sequencing. At the single-base level with Illumina data, ALE recovers 215 of 222 (97%) single nucleotide variants in a training set from a GC-rich Rhodobacter sphaeroides genome. Using real Pacific Biosciences data, ALE identifies 12 of 12 synthetic errors in a Lambda Phage genome, surpassing even Pacific Biosciences' own variant caller, EviCons. In summary, the ALE framework provides a comprehensive, reference-independent and statistically rigorous measure of single genome and metagenome assembly accuracy, which can be used to identify misassemblies or to optimize the assembly process. AVAILABILITY ALE is released as open source software under the UoI/NCSA license at http://www.alescore. org. It is implemented in C and Python.