Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome‐wide SNP genotyping identifies the Stereocilin (STRC) gene as a major contributor to pediatric bilateral sensorineural hearing impairment

Hearing loss is the most prevalent sensory perception deficit in humans, affecting 1/500 newborns, can be syndromic or nonsyndromic and is genetically heterogeneous. Nearly 80% of inherited nonsyndromic bilateral sensorineural hearing loss (NBSNHI) is autosomal recessive. Although many causal genes have been identified, most are minor contributors, except for GJB2, which accounts for nearly 50% of all recessive cases of severe to profound congenital NBSNHI in some populations. More than 60% of children with a NBSNHI do not have an identifiable genetic cause. To identify genetic contributors, we genotyped 659 GJB2 mutation negative pediatric probands with NBSNHI and assayed for copy number variants (CNVs). After identifying 8 mild‐moderate NBSNHI probands with a Chr15q15.3 deletion encompassing the Stereocilin (STRC) gene amongst this cohort, sequencing of STRC was undertaken in these probands as well as 50 probands and 14 siblings with mild‐moderate NBSNHI and 40 probands with moderately severe‐profound NBSNHI who were GJB2 mutation negative. The existence of a STRC pseudogene that is 99.6% homologous to the STRC coding region has made the sequencing interpretation complicated. We identified 7/50 probands in the mild‐moderate cohort to have biallelic alterations in STRC, not including the 8 previously identified deletions. We also identified 2/40 probands to have biallelic alterations in the moderately severe‐profound NBSNHI cohort, notably no large deletions in combination with another variant were found in this cohort. The data suggest that STRC may be a common contributor to NBSNHI among GJB2 mutation negative probands, especially in those with mild to moderate hearing impairment. © 2011 Wiley Periodicals, Inc.
Change in degree of type 1 piliation of Escherichia coli during experimental peritonitis in the mouse

To determine whether expression of type 1 pili varies during the course of Escherichia coli infection in vivo, mice were injected intraperitoneally with 5 X 10(7) CFU of piliated or nonpiliated phase variants per ml, and the degree of piliation was measured in peritoneal exudate by an enzyme-linked immunosorbent assay inhibition method. In the animals challenged with the piliated bacteria, the numbers of organisms increased a log over 9 h and the amount of pilus antigen decreased from 3 to 0.075 micrograms/10 bacteria. After a 4-h delay, nonpiliated bacteria also increased by one log over 9 h; however, the amount of piliation remained virtually undetectable. Piliated E. coli were more virulent than nonpiliated variants in this model (50% lethal dose of 7.5 X 10(6) versus 3 X 10(7), respectively). The difference was significantly reduced by prior passive immunization with rabbit serum containing high titers of antipili antibody. Piliated bacteria adhered in significantly greater numbers to isolated mouse peritoneal membranes than did nonpiliated variants (15,400 +/- 2,700 versus 1,300 +/- 700 bacteria/mm2, respectively; P = 0.05). Adherence was inhibited by the presence of 0.1 M alpha methyl mannose (1,500 +/- 1,800 bacteria/mm2, P = 0.01). These results confirm the results of previous qualitative studies showing that phase variation of type 1 pili occurs in vivo and suggest that these pili may confer an initial advantage for growth of E. coli in the peritoneal cavity, presumably by fostering colonization of the peritoneal serosal surface.
Convergent Starvation Signals and Hormone Crosstalk in Regulating Nutrient Mobilization upon Germination in Cereals[C][W]

This work shows that not only sugar but also nitrogen and phosphate starvation signals converge with GA signaling to promote the co-nuclear import of MYBS1 and MYBGA and expression of a large set of GA-inducible but functionally distinct hydrolases, transporters, and regulators active in nutrient mobilization required for seedling growth in rice and barley. Germination is a unique developmental transition from metabolically quiescent seed to actively growing seedling that requires an ensemble of hydrolases for coordinated nutrient mobilization to support heterotrophic growth until autotrophic photosynthesis is established. This study reveals two crucial transcription factors, MYBS1 and MYBGA, present in rice (Oryza sativa) and barley (Hordeum vulgare), that function to integrate diverse nutrient starvation and gibberellin (GA) signaling pathways during germination of cereal grains. Sugar represses but sugar starvation induces MYBS1 synthesis and its nuclear translocation. GA antagonizes sugar repression by enhancing conuclear transport of the GA-inducible MYBGA with MYBS1 and the formation of a stable bipartite MYB-DNA complex to activate the α-amylase gene. We further discovered that not only sugar but also nitrogen and phosphate starvation signals converge and interconnect with GA to promote the conuclear import of MYBS1 and MYBGA, resulting in the expression of a large set of GA-inducible but functionally distinct hydrolases, transporters, and regulators associated with mobilization of the full complement of nutrients to support active seedling growth in cereals.
Biosonar resolving power: echo-acoustic perception of surface structures in the submillimeter range

The minimum distance for which two points still can be separated from each other defines the resolving power of a visual system. In an echo-acoustic context, the resolving power is usually measured as the smallest perceivable distance of two reflecting surfaces on the range axis and is found to be around half a millimeter for bats employing frequency modulated (FM) echolocation calls. Only few studies measured such thresholds with physical objects, most often bats were trained on virtual echoes i.e., echoes generated and played back by a computer; moreover, bats were sitting while they received the stimuli. In these studies differences in structure depth between 200 and 340 μm were found. However, these low thresholds were never verified for free-flying bats and real physical objects. Here, we show behavioral evidence that the echo-acoustic resolving power for surface structures in fact can be as low as measured for computer generated echoes and even lower, sometimes below 100 μm. We found this exceptional fine discrimination ability only when one of the targets showed spectral interferences in the frequency range of the bats′ echolocation call while the other target did not. This result indicates that surface structure is likely to be perceived as a spectral quality rather than being perceived strictly in the time domain. Further, it points out that sonar resolving power directly depends on the highest frequency/shortest wavelength of the signal employed.
Chromatic Stereopsis

One approach to developing faster, more robust stereo algorithms is to seek a more complete and efficient use of information available in stereo images. The use of chromatic (color) information has been largely neglected in this regard. Motivations for using chromatic information are discussed, including strong evidence for the use of chromatic information in the human stereo correspondence process in the form of a novel psychophysical experiment which we have performed. Specifically, we measured the minimum disparity needed to produce a reversal in apparent depth in ambiguous chromatic "wallpaper" stereograms. Our results indicate that chromatic information plays an important role in the stereo correspondence process when luminances variations are present. To investigate the potential role of chromatic information in computational stereo algorithms, a novel chromatic matching constraint -- the chromatic gradient matching constraint -- is presented. Then, a thorough analysis of the utility of this constraint in the PMF Algorithm is performed for a large range of sizes of the matching strength support neighborhood, and the performances of the algorithm with and without these constraints are directly compared in terms of disambiguation ability, matching accuracy and algorithm speed. The results demonstrate that chromatic information can gready reduce the matching ambiguity, while significantly increasing both matching accuracy and algorithm speed.
Anti‐CD40 plus interleukin‐4‐activated human naive B cell lines express unmutated immunoglobulin genes with intraclonal heavy chain isotype variability

Combination of anti‐CD40 antibody and interleukin‐4 (IL‐4) induces B cell clonal expansion reminiscent of the T‐dependent proliferation following antigenic challenge in vivo. We have analyzed the usage of CH genes and the presence or absence of somatic mutations within the progeny of a single human naive B cell activated with anti‐CD40+IL‐4. To address this issue, single‐cell cultures of naive (sIgD+) tonsillar B lymphocytes expressing the VH1‐restricted G8 idiotype were set up. After culture and RNA extraction, VH1+ Ig mRNA were reverse‐transcribed, amplified by polymerase chain reaction and sequenced. A single sIgD+ B cell could generate clones expressing μ, γ1, γ3 or ε, illustrating that the progeny of a single cell can express different isotypes in response to the same stimulus in vitro. The rate of somatic mutations affecting the immunoglobulin variable heavy chain gene was indistinguishable from the background of errors introduced by Taq polymerase.
Preserving Statistical Validity in Adaptive Data Analysis

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.
Longitudinal Study of Pediatric Urticaria Pigmentosa

Urticaria pigmentosa (UP) is the most common form of mastocytosis in children and is associated with systemic signs, symptoms, and triggers. To our knowledge, the effect of UP on children's quality of life has not been studied. The objective of the current study was to characterize the natural history, triggers, and complications of pediatric UP, identify prognostic indicators, and determine its effect on quality of life.
Virulence of Burkholderia mallei Quorum-Sensing Mutants

ABSTRACT Many Proteobacteria use acyl-homoserine lactone-mediated quorum-sensing (QS) to activate specific sets of genes as a function of cell density. QS often controls the virulence of pathogenic species, and in fact a previous study indicated that QS was important for Burkholderia mallei mouse lung infections. To gain in-depth information on the role of QS in B. mallei virulence, we constructed and characterized a mutant of B. mallei strain GB8 that was unable to make acyl-homoserine lactones. The QS mutant showed virulence equal to that of its wild-type parent in an aerosol mouse infection model, and growth in macrophages was indistinguishable from that of the parent strain. Furthermore, we assessed the role of QS in B. mallei ATCC 23344 by constructing and characterizing a mutant strain producing AiiA, a lactonase enzyme that degrades acyl-homoserine lactones. Although acyl-homoserine lactone levels in cultures of this strain are very low, it showed full virulence. Contrary to the previous report, we conclude that QS is not required for acute B. mallei infections of mice. QS may be involved in some stage of chronic infections in the natural host of horses, or the QS genes may be remnants of the QS network in B. pseudomallei from which this host-adapted pathogen evolved.
Getting Cold Start Users Connected in a Recommender System's Trust Network

Generating personalized recommendations for new users is particularly challenging, because in this case, the recommender system has little or no user record of previously rated items. Connecting the newcomer to an underlying trust network among the users of the recommender system alleviates this socalled cold start problem. In this paper, we study the effect of guiding the new user through the connection process, and in particular the influence this has on the amount of generated recommendations. Experiments on a dataset from Epinions.com support the claim that it is more beneficial for a newcomer to connect to an identified key figure instead of to a random user.
Sex, Death, and the Red Queen

Experiments involving host-parasite interactions demonstrate the evolutionary benefits of sexual reproduction. Sex is hard to explain. Since males can't reproduce by themselves and often contribute nothing except genes to offspring, a population of asexual females can grow at double the rate of a population that reproduces sexually (1). Why then, given this “cost of males,” do most plants and animals indulge in biparental sex? One possible solution is that sex accelerates adaptation; the Red Queen hypothesis, for example, proposes that sex gives plants and animals an edge in the never-ending battle against their coevolving parasites (2–4). Although researchers have collected empirical field data consistent with the Red Queen hypothesis from a range of natural host-parasite systems, direct experimental evidence that coevolving parasites select for sex in their hosts has proven elusive. On page 216 of this issue, Morran et al. (5) pin down some of that direct evidence. In laboratory experiments, they grew several populations of nematode worms, some with and some without a bacterial parasite, to provide the most definitive support yet for the Red Queen's answer to why sex evolved.
Detecting Analogies Unconsciously

Analogies may arise from the conscious detection of similarities between a present and a past situation. In this functional magnetic resonance imaging study, we tested whether young volunteers would detect analogies unconsciously between a current supraliminal (visible) and a past subliminal (invisible) situation. The subliminal encoding of the past situation precludes awareness of analogy detection in the current situation. First, participants encoded subliminal pairs of unrelated words in either one or nine encoding trials. Later, they judged the semantic fit of supraliminally presented new words that either retained a previously encoded semantic relation (“analog”) or not (“broken analog”). Words in analogs versus broken analogs were judged closer semantically, which indicates unconscious analogy detection. Hippocampal activity associated with subliminal encoding correlated with the behavioral measure of unconscious analogy detection. Analogs versus broken analogs were processed with reduced prefrontal but enhanced medial temporal activity. We conclude that analogous episodes can be detected even unconsciously drawing on the episodic memory network.
Stress, appraisal and coping following mild traumatic brain injury

Purpose: The present study tested a portion of the stress, appraisal and coping (SAC) model proposed by Godfrey, Knight and Partridge. Methods: Using data gathered from 94 individuals who had sustained a traumatic brain injury, path analysis results indicated that a model based on Godfrey et al.'s SAC model did not fit the sample data. Based on relevant statistical output, previous research and theory, a re-specified model was tested. Results: The final model was shown to meet common statistical measures for establishing model fit. The final model indicated that higher levels of perceived stress were predictive of higher levels of self-reported depression, higher levels of depression were predictive of lower levels of dispositional hope and dispositional hope was predictive of increased life satisfaction and work productivity. Conclusions: The present findings hold implications for both research and for clinical practice. The findings do suggest the need for additional research to further clarify factors that contribute to emotional adjustment following traumatic brain injury.
Validation of information recorded on general practitioner based computerised data resource in the United Kingdom.

OBJECTIVE--To determine the extent of agreement between clinical information recorded on surgery computers of selected general practitioners and similar information in manual records of letters received from hospital consultants and kept in the general practitioners' files. DESIGN--Hospital consultants' letters in the manual records of selected general practitioners were photocopied and the consultants' clinical diagnoses were compared with diagnoses recorded on computer. SETTING--General practices in the United Kingdom using computers provided by VAMP Health for recording clinical information. SUBJECTS--2491 patients who received one of three non-steroidal anti-inflammatory drugs and who attended 58 practices whose computer recorded data were considered after a preliminary review to be of satisfactory quality. RESULTS--Among 1191 patients for whom consultants' letters were forwarded a clinical diagnosis reflecting the diagnosis noted on a consultant letter was present on the computer record for 1038 (87%). CONCLUSION--Clinical information available on the computer records of the general practitioners who participated in this study is satisfactory for many clinical studies.
Japanese Guidelines for the Management of Respiratory Infectious Diseases in Children 2007 with focus on pneumonia

Members of the Japanese Society of Pediatric Pulmonology and the Japanese Society for Pediatric Infectious Diseases developed the Guidelines for the Management of Respiratory Infectious Diseases in Children with the objective of facilitating the appropriate diagnosis and treatment of childhood respiratory infections. To date, a first edition (2004) and a revised edition (2007) have been issued. Many problems complicate the diagnosis of the pathogens responsible for bronchopulmonary infections in children. The Guidelines were the first pediatric guidelines in the world to recommend treatment with antimicrobials suited to causative pathogens as identified from cultures of sputum and other clinical specimens collected from infection sites and satisfying assessment criteria. The major causative microorganisms for pneumonia in infants and children were revealed to be Streptococcus pneumoniae, Haemophilus influenzae and Mycoplasma pneumoniae. This manuscript describes the Guidelines for the Management of Respiratory Infectious Diseases in Children in Japan 2007, with a focus on pneumonia.
The study of functional properties of Nypa fruticans flour

Nypafruticans or known as nypa produces considerable amount of fruit with high content of carbohydrate. The mesocarp of the mature fruit is a potential source of energy but underutilised. This research was conducted to study the production of flour from mesocarp of mature nypa fruit and to determine the functional properties of nypa flour. This research used the fruit from mangrove area in Jambi Province. The highest rendemenof flour in ratio to mesocarp weight was 20.00±5.24%. Mesocarp processing produced flour with low fat content (1.45%) and high crude fibre content (17.68%), color parameter L* 83.13±4.04, a* -0.67±0.90, and b* 4.80±0.80. OAC nypa flour was 1.20±0.20 and its WAC was 2.84±0.24. Nypaflour exhibited low swelling power and solubility. The highest swelling power and solubility were achieved at 85oC with value of 4.5g/g and 10.56% respectively.
Embedding Learning with Events in Heterogeneous Information Networks

In real-world applications, objects of multiple types are interconnected, forming <italic>Heterogeneous Information Networks</italic>. In such heterogeneous information networks, we make the key observation that many interactions happen due to some <italic>event</italic> and the objects in each event form a complete semantic unit. By taking advantage of such a property, we propose a generic framework called <italic><bold>H</bold>yper<bold>E</bold>dge- </italic><bold>B</bold><italic>ased</italic> <bold>E</bold><italic>mbedding</italic> (<sc>Hebe</sc>) to learn object embeddings with events in heterogeneous information networks, where a <italic>hyperedge</italic> encompasses the objects participating in one event. The <sc>Hebe</sc> framework models the proximity among objects in each event with two methods: (1) predicting a target object given other participating objects in the event, and (2) predicting if the event can be observed given all the participating objects. Since each hyperedge encapsulates more information of a given event, <sc>Hebe</sc> is robust to data sparseness and noise. In addition, <sc>Hebe</sc> is scalable when the data size spirals. Extensive experiments on large-scale real-world datasets show the efficacy and robustness of the proposed framework.
Combining ERPs and EEG spectral features for decoding intended movement direction

The posterior parietal cortex (PPC) plays an important role in visuomotor transformations for movement planning and execution. To investigate how noninvasive electroencephalographic (EEG) signals correlate with intended movement directions in the PPC, this study recorded whole-head EEG during a delayed saccade-or-reach task and found direction-related changes in both event-related potentials (ERPs) and the EEG power in the theta and alpha bands in the PPC. Single-trial (left versus right) classification using ERP and EEG spectral features prior to motor execution obtained an average accuracy of 65.4% and 65.6% respectively on 10 subjects. By combining the two types of features, the classification accuracy increased to 69.7%. These results show that ERP and EEG spectral power modulations contribute complementary information to decoding intended movement directions in the PPC. The proposed paradigm might lead to a practical brain-computer interface (BCI) for decoding movement intention of individuals.