Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico Analysis of 2085 Clones from a Normalized Rat Vestibular Periphery 3′ cDNA Library

The inserts from 2400 cDNA clones isolated from a normalized Rattus norvegicus vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3′ cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa’s ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5′ end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function.
Functional analysis of the FimE integrase of Escherichia coli K‐12: isolation of mutant derivatives with altered DNA inversion preferences

Phase variable expression of type 1 fimbriae in Escherichia coli arises from a site‐specific recombination event that inverts a short segment of chromosomal DNA carrying the promoter for transcription of the gene encoding the fimbrial subunit protein. Two integrase‐like recombinases are involved in switching. The FimB recombinase inverts the DNA segment in either orientation, whereas the FimE protein inverts it predominantly in the ON‐to‐OFF direction. In this paper, we report the isolation of a FimE mutant protein that has enhanced bidirectional switching activity. This protein has an arginine‐to‐lysine substitution at position 59, and this confers a FimB‐like switching character on FimE without altering its ability to bind to DNA. The arginine was not a member of the arginine‐histidine‐arginine‐tyrosine catalytic tetrad that is common to all integrase‐like recombinases. The catalytic tetrad members of FimE were identified at positions 41, 136, 139 and 171 and shown to be essential for FimE function. In addition, other amino acid residues that make important contributions to the DNA binding activity of FimE or its ON‐to‐OFF inversion efficiency were identified.
Chronic otitis media

Abstract Chronic otitis media (COM) is a common problem facing general practitioners, pediatricians and otolaryngologists. This article reviews the aetiopathogenesis, epidemiology, presentation, natural history, complications and management of COM. The literature was reviewed by using the PubMed search engine and entering a combination of terms including “COM”, “diagnosis”, “incidence”, “complications” and “management”. Relevant articles were identified and examined for content. What is the “take-home” message for the clinician? COM is a common problem with various sub-categories according to the disease state. It most commonly presents with painless otorrhoea and hearing loss. Treatment options vary according to the activity and type of disease encountered. COM carries significant patient morbidity.
On discrete functional inequalities for some finite volume schemes

We prove several discrete Gagliardo-Nirenberg-Sobolev and Poincare-Sobolev inequalities for some approximations with arbitrary boundary values on finite volume meshes. The keypoint of our approach is to use the continuous embedding of the space $BV(\Omega)$ into $L^{N/(N-1)}(\Omega)$ for a Lipschitz domain $ \Omega \subset \mathbb{R}^{N}$, with $N \geq 2$. Finally, we give several applications to discrete duality finite volume (DDFV) schemes which are used for the approximation of nonlinear and non isotropic elliptic and parabolic problems.
Results on permutations with distinct difference property

We prove that for all odd primes $p$ and positive integers $\alpha \geq 2$, a construction of Batten and Sane yields at least $(p-1)^3/4$ permutations with a distinct difference property (DDP) of $\{1,2,\ldots,p^\alpha-1\}$. This proves a conjecture of Batten and Sane, that at least $(p-1)^2/2$ such permutations exist. We also pose several research questions for DDP permutations.
Interaction Design Issues: A literature review

This paper presents an analysis on a literature review findings in Interaction Design Issues Journals from the year 2006 to 2010. Due to the limited literature review reported on Interaction Design Issues, this study is aiming to provide some input on the current topics, methods and theories, interaction design elements and future trends of research in the field of Interaction Design. We employ content analysis technique as to select words, phrases or common sentences in the articles based on Topic Classification Scheme adapted from Zhang and Li (2005). Findings from this study are fully addressed to further explore Interaction Design criteria as to improve Man Machine Interaction in the future.
Rapid development of new language pairs at SYSTRAN

One of the mottos of pure statistical MT system promoters is that it is possible to “build a new language pair” overnight, but the development of a new language pair for a proficient rule-based translator requires a great amount of effort in linguistic rules and resources description. Therefore, we are interested in rapid development techniques for rule-based systems. In this paper, we present the work that was conducted at SYSTRAN during the past year: we successfully developed 12 new language pairs in one year. This led us to shift some architecture paradigms in our translators, to expand implementations with the notion of Linguistic Families, to open our interfaces to more readable formats, and to design ways to work with fully multisource / multitarget aligned dictionaries in order to save time, in particular with the coding effort.
Molecular investigation of the human gastrointestinal ecosystem.

The gastrointestinal tract of humans is colonized soon after birth by a myriad of microbial species with a characteristic distribution that depends on specific locations. The detection and identification of many of these organisms has largely been hampered by the incomplete knowledge of their culture conditions as well as the predominance of strict anaerobes. Gastrointestinal tract ecology has been experiencing a revival due to the development of molecular techniques that bypass cultivation, especially those based on 16S ribosomal RNA genes (1). Separation of 16S ribosomal DNA (rDNA) PCR products by denaturing gradient gel electrophoresis, a rapid fingerprinting technique for complex communities, has revealed that each baby dominant microbiota is rather simple and unstable and evolves in children and adults to a complex, stable and unique state (1,2). Special attention has been focused on the bifidobacteria and the lactic acid bacterial (LAB) populations, both those that are naturally present within this complex ecosystem and those that are ingested as probiotics in functional foods. Using primers specifically directed at the rDNA of Lactobacillus and Bifidobacterium genera in combination with denaturing gradient gel electrophoresis, the indigenous species and effects of diet on the gastrointestinal tract can be rapidly monitored (3,4). In addition to the presence of the different microbial groups, the viability of the microbes in the intestinal tract may be estimated by a combination of fluorescent in situ hybridization, staining with physiological probes and flow cytometric sorting (5). Current use of DNA arrays based on the complete genome sequence of the human Lactobacillus plantarum isolate is providing opportunities to study microbiota global gene expression in relation to the intestinal environment. Overall, molecular technologies including high-throughput genomics and proteomics-based approaches can offer a wider scope for understanding of microbe-diet-host interactions that may by used to positively influence the health of the host (6).
Body temperature and locomotor capacity in a heterothermic rodent

SUMMARY We quantify the locomotor capacity of the round-tailed ground squirrel (Spermophilus tereticaudus), a mammal that can lower energetic costs by relaxing thermoregulatory limits without becoming inactive. We measured maximum sprint speed, maximum limb cycling frequency and maximum force production in animals at body temperatures ranging from 31°C to 41°C. We found no thermal dependence in any of these parameters of locomotion. Results (means ± s.e.m.) across this range of body temperatures were: sprint speed = 4.73±0.04 m s-1, limb cycling frequency = 19.4±0.1 Hz and maximum force production = 0.012±0.0003 N g-1. The neuro-muscular system of this species may thus be less thermally dependent at these temperatures than that of other mammals, allowing for the maintenance of whole-animal performance across a broader range of body temperatures. The absence of any significant loss of locomotor capabilities associated with either a decrease of 7-8°C or a rise of 3-4°C in body temperature from typical mammalian values raises significant questions regarding our understanding of the evolution and physiology of the mammalian mode of thermoregulation.
Tackling the most difficult diseases

The 1990s witnessed one of the most successful programmes to eradicate malaria by tackling its vector, the Anopheles mosquito. Its main component was the release of sterilised male mosquitoes into the environment, which competed with wild ones for the available females. By repeating this every year with ever‐increasing numbers of sterilised flies, health officials from the World Health Organization (WHO) and various countries hoped to eradicate the mosquito and thus malaria. In some parts of the world, this method indeed worked; southern Europe and large areas of Asia, North and Central America and Africa became virtually malaria free. But while Europe has remained so, the mosquitoes and the diseases they transmit have come back with a vengeance in many areas around the world. The latest data released in August 2001 show that there are now between 700 000 and 2.7 million deaths each year from malaria, 75% of which are African children. According to the Multilateral Initiative on Malaria, this is a higher mortality rate than the yearly toll of AIDS in Africa. Besides the fatalities, between 400 and 900 million acute episodes of fever occur in children under the age of five which can slow brain development and retard cognitive abilities. Anthony James, a geneticist at the University of California in Irvine, refers to malaria as ‘the most difficult vector‐borne disease to control’. Controversy abounds in the scientific community about the causes of the resurgence of these and other vector‐borne infectious diseases such as leishmaniasis, yellow fever, encephalitis and dengue fever. Theories vary from global warming to the discontinuation of the use of DDT, but as Paul Reiter from the Centers for Disease Control in Atlanta, Georgia, remarked ‘Public concern should focus on ways to deal with the realities of malaria transmission, rather than on the weather’. A number …
Spin-orbit interaction and large inelastic rates in bismuth-helium collisions

We present a combined experimental and theoretical study of cold collisions between bismuth and helium atoms in strong magnetic fields and demonstrate that the spin-orbit interaction coupling between different nonrelativistic states of Bi leads to rapid Zeeman relaxation. The Zeeman relaxation of Bi in the ground electronic state is found to be very efficient due to the admixture of electronic excited states which show an interaction anisotropy due to their nonzero electronic orbital angular momentum. Our results indicate that dense ensembles of heavy relativistic atoms will generally be unstable in magnetic traps due to significant spin relaxation induced by spin-orbit interactions.
How evolution draws trade-offs

Recent empirical evidence suggest that trade-off shapes can evolve, challenging the classica image of their high entrenchment. Here we model the evolution of the physiological mechanism that controls the allocation of resources to two traits, by mutating the expression and the conformation of its constitutive hormones and receptors. We show that trade-off shapes do indeed evolve in this model through the combined action of genetic drift and selection, such that their evolutionarily expected curvature and length depend on context. Despite this convergence at the phenotypic level, we show that a variety of physiological mechanisms may evolve in similar simulations, suggesting redundancy at the genetic level. We anticipate that more complex evolutionary scenarios should tighten this link between genotype and phenotype. This model should provide a useful framework to interpret the overly complex observations of both evolutionary endocrinology and evolutionary ecology.
Occupational Injury and Treatment Patterns of Migrant and Seasonal Farmworkers

ABSTRACT Migrant and seasonal farmworkers are thought to be at increased risk for occupational injury and illness. Past surveillance efforts that employed medical chart review may not be representative of all farmworkers, since the proportion of farmworkers using migrant health centers (MHCs) and area hospital emergency rooms (ERs) was unknown. The purpose of the current study was to determine the proportion of workers using MHCs versus other sources of occupational health care, and to use these data to correct previous occupational injury and illness rate estimates. Researchers conducted a survey of migrant and seasonal farmworkers in two sites: the Finger Lakes Region of New York and the apple, broccoli, and blueberry regions of Maine. Researchers also conducted MHC and ER medical chart reviews in these regions for comparison purposes. Proportions of occupational morbidity by treatment location were calculated from the survey, and a correction factor was computed to adjust chart review morbidity estimates for Maine and New York State. Among 1103 subjects, 56 work-related injuries were reported: 30 (53.6%) were treated at a MHC, 8 (14.3%) at an ER, 9 (16.1%) at some other location (e.g., home, relative, chiropractor), and 9 (16.1%) were untreated. Mechanisms of injuries treated at MHCs versus all other sources did not differ significantly. The survey-based multiplier (1.87) was applied to previous statewide MHC chart review injury counts from Maine and New York. The corrected injury rates were 7.9 per 100 full-time equivalents (FTE) per year in Maine, and 11.7 per 100 FTE in New York. A chart-review based surveillance system, combined with a correction factor, may provide an effective method of estimating occupational illness and injury rates in this population.
Death Anxiety and Quality of Life in Iranian Caregivers of Patients With Cancer

Background: Concerns about death may alienate and negatively impact communication among family members of patients with life-threatening illness. Little is known about the relationship of death anxiety to quality of life in cancer family caregivers. Objective: The aim of this study was to examine relationships between sociodemographic and patient-related factors, social support, and religiosity with death anxiety and quality of life in Iranian cancer family caregivers. Methods: Three hundred thirty family caregivers from an urban regional cancer institute in Iran participated in a descriptive-correlational study that incorporated sociodemographic surveys and validated death anxiety (Templer Scale) and Quality of life (Family Version) instruments. Results: Caregivers reported moderate levels of death anxiety and decrements in QOL. Quality of life was inversely associated with death anxiety (r = −0.30, P < .001). Female caregivers who were daughters had higher death anxiety, whereas male caregivers who were sons reported higher quality of life. Conclusions: Death anxiety is associated with lowered quality of life in Iranian family caregivers. Multiple factors may impact death anxiety and quality of life relevant to the socioreligious milieu. Implications for Practice: Addressing concerns that increase death anxiety may improve quality of life and lower stress associated with adapting to the family caregiver role. Caregiving responsibilities, added to challenges associated with personal, family, and professional life, impact multiple aspects of QOL. As nurses increasingly care for patients from diverse backgrounds, it becomes more imperative that support for family caregivers that promotes psychological adaptation and quality of life is needed.
Effects of N-acetylcysteine upon the rat serum enzyme changes in skeletal muscle ischemia reperfusion

Skeletal muscle ischemia reperfusion injuries can occur with diseases, trauma and during surgical procedures. Ischemia reperfusion injury is characterized by the production of oxygen free radicals leading to disturbances in vasomotility and microvascular permeability. The objective was to evaluate effects of N-acetylcysteine as a scavenger of radical oxygen species on the serum enzyme changes secondary to muscle ischemia reperfusion. Twenty wistar male rats were divided randomly into two experimental groups: group ischemia-reperfusion (group I) and group ischemia-reperfusion + N-acetylcysteine (group II). After ketamine (50 mgkg-1) and xylazine (10 mgkg-1) anesthesia, femoral artery was exposed and undergone 2h of ischemia, 24h of reperfusion. Rats that were treated with N-acetylcysteine given intravenously at a dose of 150 mgkg-1, immediately before reperfusion. After 24h of reperfusion, the blood samples were collected and submitted for evaluation of serum aspirate aminotransferase (AST), alanine aminotransferase (ALT), creatine phosphokinase (CPK), lactate dehrdrogenase (LDH) values to identify the ischemic damage occurring in the skeletal muscle tissue. Enzymatic parameters (CPK, AST, ALT and LDH) measured for demonstrating ischemia induced muscle injuries were lower in the group receiving Nacetylcysteine. In this study, N-acetylcysteine as an antioxidant substance was demonstrated to have protective effects on acute ischemia and reperfusion injury of the skeletal muscle in lower extremities.
CO/FT Regulatory Module Controls Timing of Flowering and Seasonal Growth Cessation in Trees

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day–induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.
Crigler‐Najjar syndrome type I in Tunisia may be associated with a founder effect related to the Q357R mutation within the UGT1 gene

Jeanne Francoual, Armelle Rivierre, Chahnez Mokrani, Naïma Khrouf, Frédéric Gottrand, Anne Myara, Béatrice Le Bihan, Liliane Capel, Albert Lindenbaum, and Philippe Labrune* Laboratoire de Biochimie, Hôpital Antoine Béclère (AP-HP), Clamart, France Service de Pédiatrie, Hôpital Antoine Béclère (AP-HP), Clamart, France Laboratoire de Biochimie, Hôpital Saint-Joseph, Paris, France Service de Pédiatrie, Hôpital Jeanne de Flandre, Lille, France Centre de Maternité et de Neonatologie de Tunis, El Jebri, Tunisia
RETINAL DETACHMENT IN HIGHLY MYOPIC EYES DUE TO MACULAR HOLES AND EPIRETINAL TRACTION

We operated on four highly myopic eyes with recurrent retinal detachment due to macular holes. A thin layer of epiretinal tissue was present over the posterior retina in each eye, probably causing tangential traction on the retina and accounting for the recurrent detachment. Biopsy of the tissue from one case showed mainly acellular material resembling cortical vitreous. Recognizing this clinical condition may permit successful treatment of certain cases with recurrent retinal detachment in highly myopic eyes with macular holes.
Sequences in the 5′ and 3′ R Elements of Human Immunodeficiency Virus Type 1 Critical for Efficient Reverse Transcription

ABSTRACT The genome of human immunodeficiency virus type 1 (HIV-1) contains two direct repeats (R) of 97 nucleotides at each end. These elements are of critical importance during the first-strand transfer of reverse transcription, during which the minus-strand strong-stop DNA (−sssDNA) is transferred from the 5′ end to the 3′ end of the genomic RNA. This transfer is critical for the synthesis of the full-length minus-strand cDNA. These repeats also contain a variety of other functional domains involved in many aspects of the viral life cycle. In this study, we have introduced a series of mutations into the 5′, the 3′, or both R sequences designed to avoid these other functional domains. Using a single-round infectivity assay, we determined the ability of these mutants to undergo the various steps of reverse transcription utilizing a semiquantitative PCR analysis. We find that mutations within the first 10 nucleotides of either the 5′ or the 3′ R sequence resulted in virions that were markedly defective for reverse transcription in infected cells. These mutations potentially introduce mismatches between the full-length −sssDNA and 3′ acceptor R. Even mutations that would create relatively small mismatches, as little as 3 bp, resulted in inefficient reverse transcription. In contrast, virions containing identically mutated R elements were not defective for reverse transcription or infectivity. Using an endogenous reverse transcription assay with disrupted virus, we show that virions harboring the 5′ or the 3′ R mutations were not intrinsically defective for DNA synthesis. Similarly sized mismatches slightly further downstream in either the 5′, the 3′, or both R sequences were not detrimental to continued reverse transcription in infected cells. These data are consistent with the idea that certain mismatches within 10 nucleotides downstream of the U3-R junction in HIV-1 cause defects in the stability of the cDNA before or during the first-strand transfer of reverse transcription leading to the rapid disappearance of the −sssDNA in infected cells. These data also suggest that the great majority of first-strand transfers in HIV-1 occur after the copying of virtually the entire 5′ R.