Miracle-dz/UniFAR-FTUs huggingface dataset:
New Methodology for Measuring Semantic Functional Similarity Based on Bidirectional Integration

1.2 billion users in Facebook, 17 million articles in Wikipedia, and 190 million tweets per day have demanded significant increase of information processing through Internet in recent years. Similarly life sciences and bioinformatics also have faced issues of processing Big data due to the explosion of publicly available genomic information resulted from the Human Genome Project (HGP) and the increasing usage of high throughput technology. HGP was completed in 2003 and resulted in identifying 20,000-25,000 genes in human DNA and determining the sequences of three billion human base pairs. The information requires huge amount of data storage and becomes difficult to process using on-hand database management tools or traditional data processing applications. This thesis introduces new method, Biological and Statistical Mean (BSM) score to calculate functional similarity between gene products (GPs) that can help to extract biologically relevant and statistically robust information from large-scale biomedical, genomic and proteomic data sources. BSM score is defined by 16 different scoring matrices derived from principles of multi-view learning in machine learning algorithm and five different databases including Gene Ontology, UniProt, SCOP, CATH, and KUPS. The proposed method also shows how diverse databases and principles in machine learning theory can be integrated into a simple scoring function, and how the simple concept can give significant impact on the studies in biomedical and human life sciences. The comprehensive evaluations and performance comparisons with other conventional methods show that BSM score clearly outperforms other methods in terms of sensitivity of clustering similarity functional groups and coverage of identifying related genes. As a part of potential applications handling large amount of diverse data sources in medical domain, this thesis introduces similarity-based drug target identification and disease networks using BSM scores. Application of BSM score is freely available through http://www.ittc. ku.edu/chenlab/goal/
A holistic approach to fault management: wheels within a wheel

Systems with high dependability requirements are increasingly relying on complex on-line fault management systems to function in a wide range of scenarios. Fault management systems involve a combination of multiple steps { monitoring, data analysis, planning and execution { that are typically independently developed and optimized. We argue that it is inecient and ineective to improve any particular fault management step without taking into account its interactions and dependencies with the rest of the steps. Through six real-life examples, we demonstrate this ineciency and how it results in systems that either under-perform or are over-budget. We propose instead a holistic approach to fault management that is aware of, respects, and explicitly considers, the couplings between the dierent
Recognition of spatial dynamics for predicting social interaction

We present a user study and dataset designed and collected to analyze how humans use space in face-to-face interactions. In a proof-of-concept investigation into human spatial dynamics, a Hidden Markov Model (HMM) was trained over a subset of features to recognize each of three interaction cues-initiation, acceptance, and termination-in both dyadic and triadic scenarios; these cues are useful in predicting transitions into, during, and out of multi-party social encounters. It is shown that the HMM approach performed twice as well as a weighted random classifier, supporting the feasibility of recognizing and predicting social behavior based on spatial features.
Estimating mean weighted temperature of the atmosphere for Global Positioning System applications

A water-vapor-weighted vertically averaged mean temperature of the atmosphere, Tm, is a key parameter in the retrieval of total water content from the measurements of Global Positioning System signal delays. The accuracy of precipitable water estimates is proportional to the accuracy of Tm. The geographic and seasonal variability of Tm based on 23 years of radiosonde soundings at 53 globally distributed stations is presented. Several methods for estimating Tm were evaluated by comparing the estimates against the actual Tm values. Sitespecific climatology or site-specific linear regression was superior to the geographically and seasonally invariant regression relationship typically used to estimate Tm. Relative errors at most stations were less than 2%, which corresponds to absolute errors of precipitable water of 0.1–0.5 mm The station-specific linear regression was superior to climatological means as an estimator except in the tropics, where correlations between Tm and Tsfc were not high. Also, a physical model was developed to indicate the relationship between Tm and other commonly used atmospheric variables.
Leaking Pipes Recharge Ground Water

Water is piped beneath cities in water mains, sewers, and storm drains. Most, if not all, of these pipe networks leak. Evidence from a ground-water resources study for Lima, Peru and a slope stability study in Hong Kong is presented to show that leakage losses recharge ground water. The contribution of leakage to recharge is shown by ground-water levels, ground-water chemistry, and by water balance and ground-water modeling studies. Estimates of the leakage quantities involved can be developed from water balance and modeling studies, and from analysis of conventional leakage detection tests carried out by water-supply authorities. In Lima, about 40% of the average supply became recharge. Maximum areal rates of recharge for both cities were about 3000 mm/yr.
New Technologies Smart, or Harm Work-Family Boundaries Management? Gender Differences in Conflict and Enrichment Using the JD-R Theory

Background: The relationship between technology-assisted supplemental work and well-being outcomes is a recent issue in scientific literature. Whether the use of technology for work purpose in off-work time may have a positive or negative impact on work-family balance remains an open question and the role of gender in this relationship is poorly understood. Aim: According to the JD-R theory, this study aimed to investigate the relationship between off-work hours technology assisted job demand (off-TAJD) and both work-family conflict (WFC) and work-family enrichment (WFE). Moreover, it considered two general job demands, workload and emotional dissonance, and one job resource, supervisory coaching. Method: The hypotheses were tested with a convenience sample of 671 workers. Data were collected with a self-report questionnaire and analyzed with SPSS 23 and through multi-group structural equation model (SEM) (Mplus 7). Results: The estimated SEM [Chi-square (510) = 1041.29; p < 0.01; CFI = 0.95; TLI = 0.95; RMSEA = 0.06 (0.05, 0.06); SRMR = 0.05. M = 319/F = 352] showed that off-TAJD was positively related to WFC in both subsamples; off-TAJD was positively related also to WFE only in the Male group. Workload was positively related to WFC in both Male and Female subsamples. Emotional dissonance was positively related to WFC in both subsamples and was negatively related to WFE. Supervisory coaching was strongly, positively related to WFE in both groups, and only in the Male subsample presented a low negative relationship with WFC. Conclusion: This study contributes to the literature on new challenges in work-life interface by analyzing the association between off-TAJD and WFC and Enrichment. Our findings suggest it is important to pay attention to gender differences in the study of the impact of supplemental work carried out during off-work hours using technology on the work-life interface. In fact, employee perception of Company demands of being available during off-work time, with the use of technology, may have different consequences for men and women, indicating potential differences in the centrality of the working role. Practical implications, at both cultural and organizational levels, should address the use of technology during leisure time.
Substitutions in the Eyelet Region Disrupt Cefepime Diffusion through the Escherichia coli OmpF Channel

ABSTRACT The Escherichia coli OmpF porin is a nonspecific channel involved in the membrane translocation of small hydrophilic molecules and especially in the passage of β-lactam antibiotics. In order to understand the dynamic of charged-compound uptake through bacterial porins, specific charges located in the E. coliOmpF channel were mutated. Substitutions G119D and G119E, inserting a protruding acidic side chain into the pore, decreased cephalosporin and colicin susceptibilities. Cefepime diffusion was drastically altered by these mutations. Conversely, substitutions R132A and R132D, changing a residue located in the positively charged cluster, increased the rate of cephalosporin uptake without modifying colicin sensitivity. Modelling approaches suggest that G119E generates a transverse hydrogen bond dividing the pore, while the two R132 substitutions stretch the channel size. These charge alterations located in the constriction area have differential effects on cephalosporin diffusion and substantially modify the profile of antibiotic susceptibility.
Effects of soil moisture and temperature on NO, NO2, and N2O emissions from European forest soils

[1] Emissions of NO, NO2, and N2O to the atmosphere were measured with a fully automated laboratory system from undisturbed soil columns obtained from five different temperate and one boreal forest sites. The soils were chosen to cover a transect through Europe, sandy and loamy textures, and different atmospheric nitrogen deposition rates. In a two-factorial experimental design, soil cores were kept under varying conditions with respect to temperature (range 5–20°C) and soil moisture (range 0–300 kPa). The combination of soil temperature and soil moisture could explain a better part of variations in NO (up to 74%) and N2O (up to 86%) emissions for individual soils, but average emissions differed significantly between various forest soils. Generally, NO and N2O were emitted from all soils except from the boreal pine forest soil, where NO was consumed. NO emissions from the German spruce forest receiving highest yearly nitrogen inputs of >35 kg ha−1 yr−1 ranged from 1.3 to 608.9 μg NO-N m−2 h−1 and largely exceeded emissions from other soils. Average N2O emissions from this soil tended also to be highest (171.7 ± 42.2 μg N2O-N m−2 h−1), but did not differ significantly from other soils. NO2 deposition occurred in all soils and strongly correlated to NO emissions. NO and N2O emissions showed a positive exponential relationship to soil temperature. With activation energies between 57 and 133 kJ mol−1, N2O emissions from the various soils responded more uniformely to temperature than NO emissions with 41 and 199 kJ mol−1. The two Austrian beech forest soils showed exceptionally high activation energies for NO emissions, which might be attributed to chemodenitrification. N2O emissions increased with increasing water filled pore space (WFPS) or decreasing water tension, respectively. Maximal N2O emissions were measured between 80 and 95% WFPS or 0 kPa water tension. Optimal moisture for NO emission differed significantly between the soils, and ranged between 15% WFPS in sandy Italian floodplain soil and 65% in loamy Austrian beech forest soils. These differences may be related to the specific adaptation of the microbial communities to draught conditions.
Cheating and plagiarism: perceptions and practices of first year IT students

A study of cheating and plagiarism using a scenario based format, has provided an insight into attitudes towards questionable work practices of first year information technology students' within the School of Computer Science and Software Engineering of Monash University, and the School of Information Technology of Swinburne University. Students at both institutions showed similar responses to a range of cheating behaviours, in line with other literature. Plagiarism and cheating are widely tolerated and commonly practised, at least on the lower end of the spectrum of seriousness. However there were some areas of significant difference between the two student samples that warrant further research to develop strategic approaches for limiting cheating practices.
Vascular Endothelial Growth Factor Secretion from Pituitary Folliculostellate Cells: Role of KATP Channels

Vascular endothelial growth factor (VEGF) is an endothelial cell mitogen responsible for physiological and pathological angiogenesis. Abnormal regulation of VEGF expression in anterior pituitary folliculostellate (FS) cells has been implicated in pituitary tumour progression. FS and endocrine cells express VEGF, which is considered to be secreted by the constitutive pathway. The present study investigated the mechanism of VEGF secretion in TtT/GF cells, a mouse FS cell line. TtT/GF cells were shown to express VEGF164, the most potent and bioavailable isoform of VEGF. Immunofluorescence and immunogold electron microscopy localised VEGF to the cytoplasm and small electron‐lucent vesicles. Pituitary adenylate cyclase‐activating polypeptide (PACAP), a well‐documented stimulant of VEGF secretion, caused a robust increase in VEGF secretion over 24 h. Glyburide, an ABCA1 and KATP channel blocker, also caused an increase in VEGF secretion when applied alone, and amplified the response to PACAP. Other ABCA1 transport blockers did not affect VEGF secretion. Exposure of TtT/GF cells to cycloheximide with PACAP or glyburide inhibited the increased secretion of VEGF, consistent with control of secretion at the transcription level. The SUR2B/Kir6.1 form of KATP channels was shown to be expressed by TtT/GF cells. Diazoxide, a KATP activator, inhibited PACAP‐ and PACAP + glyburide‐stimulated VEGF secretion but not that of glyburide alone. These data suggest that KATP channels are expressed by FS cells and play a significant role in the control of VEGF secretion, and also that activation of KATP channels inhibits the secretion of VEGF at the level of transcription.
When Is a Fracture Not “Fresh”? Aligning Reimbursement With Patient Outcome After Treatment With Low-Intensity Pulsed Ultrasound

Objective: The clinical value of low-intensity pulsed ultrasound (LIPUS) for fresh fracture is known. Yet, in the absence of a definition of what “fresh” is, payers have adopted study inclusion criteria drawn from randomized clinical trials as de facto definitions of which patients should be treated, with “fresh” defined as <1 week old. Patients with fracture may thus be ineligible for LIPUS treatment after week 1, which potentially denies access to patients who could benefit from LIPUS. We seek to characterize the inflection point at which heal rate declines. Design: Prospective cohort. Setting: Food and Drug Administration–mandated nationwide postmarketing surveillance registry. Patients: Observational cohort of 5983 registry enrollees. Intervention: LIPUS, 20 min/d. Main Outcome Measure: Fracture heal rate. Logistic regression was used to model the odds ratio of nonunion from week 1 to week 12. Covariates in the model included age, gender, body mass index, open fracture, and smoking. Results: We estimated the time point at which a fracture responds to LIPUS as well as during the first week after fracture. There was significant bone-to-bone variation; metatarsal was “fresh” until week 7, ankle until week 9, humerus until week 10, and femur and radius until week 12. Healing was significantly impacted by patient age, body mass index, and open fracture (all, P ⩽ 0.02). Conclusions: Our results suggest that fractures of the metatarsal, femur, humerus, ankle, and radius respond to LIPUS treatment, as if they were still fresh at least 6 weeks longer than the eligibility allowed under current coverage policies. Level of Evidence: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Sexual and reproductive behaviour of Drosophila melanogaster from a microclimatically interslope differentiated population of ‘Evolution Canyon’ (Mount Carmel, Israel)

The strong microscale interslope environmental differences in ‘Evolution Canyon’ provide an excellent natural model for sympatric speciation. Our previous studies revealed significant slope–specific differences for a fitness complex of Drosophila. This complex involved either adaptation traits (tolerance to high temperature, different viability and longevity pattern) or behavioural differentiation, manifested in habitat choice and non–random mating. This remarkable differentiation has evolved despite a very small interslope distance (a few hundred metres only). Our hypothesis is that strong interslope microclimatic contrast caused differential selection for fitness–related traits accompanied by behavioural differentiation and reinforced by some sexual isolation, which started incipient speciation. Here we describe the results of a systematic analysis of sexual behaviour in a non–choice situation and several reproductive parameters of D. melanogaster populations from the opposite slopes of ‘Evolution Canyon’. The evidence indicates that: (i) mate choice derives from differences in mating propensity and discrimination; (ii) females from the milder north–facing slope discriminate strongly against males of the opposite slope; (iii) both sexes of the south–facing slope display distinct reproductive and behavioural patterns with females showing increased fecundity, shorter time before remating and relatively higher receptivity, and males showing higher mating propensity. These patterns represent adaptive life strategies contributing to higher fitness.
Effect of Healthcare-Acquired Infection on Length of Hospital Stay and Cost

Objective. To estimate the independent effect of a single lower respiratory tract infection, urinary tract infection, or other healthcare-acquired infection on length-of-stay and variable costs and to demonstrate the bias from omitted variables that is present in previous estimates. Design. Prospective cohort study. Setting. A tertiary care referral hospital and regional district hospital in southeast Queensland, Australia. Patients. Adults aged 18 years or older with a minimum inpatient stay of 1 night who were admitted to selected clinical specialities. Results. Urinary tract infection was not associated with an increase in length of hospital stay or variable costs. Lower respiratory tract infection was associated with an increase of 2.58 days in the hospital and variable costs of AU$24, whereas other types of infection were associated with an increased length of stay of 2.61 days but not with variable costs. Many other factors were found to be associated with increased length of stay and variable costs alongside healthcare-acquired infection. The exclusion of these variables caused a positive bias in the estimates of the costs of healthcare-acquired infection. Conclusions. The existing literature may overstate the costs of healthcare-acquired infection because of bias, and the existing estimates of excess costs may not make intuitive sense to clinicians and policy makers. Accurate estimates of the costs of healthcare-acquired infection should be made and used in appropriately designed decision-analytic economic models (ie, cost-effectiveness models) that will make valid and believable predictions of the economic value of increased infection control.
Body wave spectra from propagating shear cracks.

An earthquake source model studied in this paper predicts a higher value of P wave corner frequency than S wave corner frequency; the ratio of P to S wave corner frequency is about 1.3 on the average. This result owes mainly to the slip characteristics on the fault, that is, the center of the fault slips for a longer time than the edges and consequently a greater relative displacement takes place near the center. Relationships of source dimension with the corner frequencies for P and S waves are derived to estimate the source dimension of earthquakes from teleseismic body wave spectra. The far-field spectra from the present model of equidimensional rupture propagation demonstrate the spectral decay of ω-2 at high frequencies. The seismic efficiency is found to be independent of the size of source dimension and expressed as a function of initial stress, stress drop, and rupture velocity. Being interpreted in terms of this model, the ratio of frictional stress to final stress can be estimated from observations of rupture velocity.
Interaction Styles in Alice: Notes and Observations from Computer Animation Workshops

After several years conducting workshops on computer animation with Alice, a free platform for three dimensional computer animation created by Carnegie Mellon University, a pattern of styles of use was detected. It appears that participants in such workshops engage with the platform in one of four ways: 1) following instructions and copying the animation that the instructor is showing, 2) creating rich and visually attractive scenes with little or no movement, 3) inventing dialogue-based stories and placing characters in the scene to act them, and 4) scripting complex movement-rich scenes that use advanced features of Alice. In this paper we recount how we came to notice the patterns, describe the styles in detail, propose a process to validate their consistency across groups and events, and discuss why studying these styles could be relevant and revealing.
Cell Lineage Mapping of Taste Bud Cells and Keratinocytes in the Mouse Tongue and Soft Palate

The epithelium of the mouse tongue and soft palate consists of at least three distinct epithelial cell populations: basal cells, keratinized cells organized into filiform and fungiform papillae, and taste receptor cells present in tight clusters known as taste buds in the fungiform and circumvallate papillae and soft palate. All three cell types develop from the simple epithelium of the embryonic tongue and palate, and are continually replaced in the adult by cell turnover. Previous studies using pulse‐chase tritiated thymidine labeling in the adult mouse provided evidence for a high rate of cell turnover in the keratinocytes (5–7 days) and taste buds (10 days). However, little is known about the localization and phenotype of the long‐term stem or progenitor cells that give rise to the mature taste bud cells and surrounding keratinocytes in these gustatory tissues. Here, we make use of a tamoxifen‐inducible K14‐CreER transgene and the ROSA26 LacZ reporter allele to lineage trace the mature keratinocytes and taste bud cells of the early postnatal and adult mouse tongue and soft palate. Our results support the hypothesis that both the pore keratinocytes and receptor cells of the taste bud are derived from a common K14+K5+Trp63+Sox2+ population of bipotential progenitor cells located outside the taste bud. The results are also compatible with models in which the keratinocytes of the filiform and fungiform papillae are derived from basal progenitor cells localized at the base of these structures. STEM CELLS 2009;27:442–450
Answering Yes/No Questions via Question Inversion

This paper investigates a solution to yes/no question answering, which can be mapped to the task of determining the correctness of a given proposition. Generally it is hard to obtain explicit evidence to conclude a proposition is false from an information source, so we convert this task to a set of factoid-style questions and use an existing question answering system as a subsystem. By aggregating the answers and confidence values from a factoid-style question answering system we can determine the correctness of the entire proposition or the substitutions that make the proposition false. We evaluated the system on multiple-choice questions from a university admission test on world history, and found it to be highly accurate.