Miracle-dz/UniFAR-FTUs huggingface dataset:
Influenza A H5N1 Immigration Is Filtered Out at Some International Borders

Background Geographic spread of highly pathogenic influenza A H5N1, the bird flu strain, appears a necessary condition for accelerating the evolution of a related human-to-human infection. As H5N1 spreads the virus diversifies in response to the variety of socioecological environments encountered, increasing the chance a human infection emerges. Genetic phylogenies have for the most part provided only qualitative evidence that localities differ in H5N1 diversity. For the first time H5N1 variation is quantified across geographic space. Methodology and Principal Findings We constructed a statistical phylogeography of 481 H5N1 hemagglutinin genetic sequences from samples collected across 28 Eurasian and African localities through 2006. The MigraPhyla protocol showed southern China was a source of multiple H5N1 strains. Nested clade analysis indicated H5N1 was widely dispersed across southern China by both limited dispersal and long distance colonization. The UniFrac metric, a measure of shared phylogenetic history, grouped H5N1 from Indonesia, Japan, Thailand and Vietnam with those from southeastern Chinese provinces engaged in intensive international trade. Finally, H5N1's accumulative phylogenetic diversity was greatest in southern China and declined beyond. The gradient was interrupted by areas of greater and lesser phylogenetic dispersion, indicating H5N1 migration was restricted at some geopolitical borders. Thailand and Vietnam, just south of China, showed significant phylogenetic clustering, suggesting newly invasive H5N1 strains have been repeatedly filtered out at their northern borders even as both countries suffered recurring outbreaks of endemic strains. In contrast, Japan, while successful in controlling outbreaks, has been subjected to multiple introductions of the virus. Conclusions The analysis demonstrates phylogenies can provide local health officials with more than hypotheses about relatedness. Pathogen dispersal, the functional relationships among disease ecologies across localities, and the efficacy of control efforts can also be inferred, all from viral genetic sequences alone.
Monitoring Distributed Real-Time Systems: A Survey and Future Directions

Runtime monitors have been proposed as a means to increase the reliability of safety-critical systems. In particular, this report addresses runtime monitors for distributed hard real-time systems. This class of systems has had little attention from the monitoring community. The need for monitors is shown by discussing examples of avionic systems failure. We survey related work in the field of runtime monitoring. Several potential monitoring architectures for distributed real-time systems are presented along with a discussion of how they might be used to monitor properties of interest.
The Effects of Fabp7 and Fabp5 on Postnatal Hippocampal Neurogenesis in the Mouse

New neurons are continually produced after birth from neural stem/progenitor cells (NSCs/NPCs) in the hippocampal dentate gyrus (DG). Recent studies have reported that fatty acid binding protein 7 (Fabp7/brain lipid binding protein (BLBP)) is required for the maintenance of embryonic NSCs/NPCs and have identified an association between the Fabp7 gene and behavioral paradigms that correlate with hippocampal functions. However, the specific roles of Fabps in postnatal neurogenesis remain unknown. Herein, we demonstrate the effects of Fabp7, and another Fabp, Fabp5, on postnatal neurogenesis. Fabp7 and Fabp5 were detected in the subgranular zone (SGZ) of the DG, and Fabp7+ cells were less differentiated than Fabp5+ cells. We analyzed the differentiation state of NSCs/NPCs in the SGZ of 4‐week‐old (4w) Fabp7 knockout (7KO), Fabp5 KO (5KO), and Fabp7/Fabp5 double KO (7/5KO) mice and found that the number of NSCs/NPCs was dramatically reduced compared with wild‐type mice. Although the uptake of BrdU 1 day after injection was decreased in all KO mice, the survival of BrdU+ cells 1 month after injection was increased in the 7/5KO mice compared to other three genotypes. We also observed an enhancement of neuronal differentiation in all Fabp KO mice. In addition, the proliferation and survival of NSCs/NPCs differed along the anterior‐posterior axis (A‐P axis). A greater number of newborn cells in the posterior region became extinct, but this tendency was not apparent in the Fabps KO mice. These data suggest that Fabp7 and Fabp5 have differential roles for proliferation and survival of the NSCs/NPCs during postnatal DG neurogenesis. STEM Cells2012;30:1532–1543
Isolation and characterization of a ColE1-like plasmid from Enterobacter agglomerans with a novel variant of rom gene.

Complete nucleotide sequence of a plasmid isolated from Enterobacter agglomerans has been determined. The plasmid, called pPIGDM1, consists of 2495 base pairs. The analysis of its nucleotide sequence suggested that pPIGDM1 may be a ColE1-like replicon. We confirmed this hypothesis by constructing a pPIGDM1-derived plasmid harboring the cat gene (pBW4), which could be introduced into Escherichia coli cells, and demonstrating that pBW4 cannot replicate in the absence of the polA function and that its copy number is significantly decreased in the pcnB mutant. Like some other ColE1-type replicons (e.g., pBR322), pPIGDM1-derived plasmids can be amplified both by chloramphenicol method and in isoleucine-starved relA mutants but not in relA+ bacteria. Inactivation of the putative rom gene by insertion of an amplicillin-resistance gene resulted in significant increase in pPIGDM1-derived plasmid copy number in E. coli-despite the fact that amino acid sequence of the putative RNA 1 modulator (Rom) protein is only 55.7% identical to the ColE1 analog. The pPIGDM1-derived rom-like coding sequence is also homologous to the rom-like gene present in the Proteus vulgaris plasmid pPvul. We suggest to group all these gene products into a new family called ROMS (RNA one modulators). Since a pPIGDM1-derived plasmid is compatible with other ColE1-like replicons (pMB1-, p15A, RSF1030-, and CloDF13-derived) in E. coli, one may consider pPIGDM1 as a progenitor of new cloning vehicles compatible with most (if not all) of currently used plasmid vectors. Moreover, this plasmid may serve as a source of the new rom-like gene coding for a protein useful in investigation of RNA-protein interactions. A role for the pPIGDM1 plasmid in the host strain is not known.
Barroom aggression among Australian tradesmen: associations with heavy episodic drinking, trait aggression, and conformity to masculine norms

Abstract Objective: Past research associates heavy episodic drinking (HED), trait aggression, and conformity to masculine norms with increased risk of barroom aggression (BA) perpetration by men. Such studies have mostly employed university samples, limiting the generalizability of these findings to other male groups. This study assessed the association of HED, trait aggression, and masculine norms with BA perpetration in a sample of male tradespeople. Method: Australian tradesmen aged 18–35 years (N = 221, Mage = 21.92, SDage = 4.08, 81.5% apprentices) completed an individual interview at their place of work or training, assessing past-month HED and past-year verbal and physical BA perpetrations, as well as the short Buss-Perry Aggression Questionnaire and items from the Conformity to Masculine Norms Inventory-46. Results: Participants reported high levels of verbal (35.1%) and physical (27%) BA perpetration. Negative binomial regression analyses found that HED, trait aggression, and Winning, Risk-taking, and Playboy norms predicted increased risk of both verbal and physical BA perpetrations, while Violence was negatively associated with verbal BA perpetration. Conclusions: Trait aggression was the strongest predictor of both verbal and physical BA perpetrations. Dispositional aggression, HED, and norms endorsing competitiveness, risk-taking, and promiscuity increase the risk of male tradespeople engaging in BA.
Evaluation of Vertical Accuracy of the WorldDEM™ Using the Runway Method

Accuracy assessment of a global digital elevation model (DEM) is an important and challenging task primarily because of the difficulties and costs associated with securing a reliable and representative reference dataset. In this article, we report on the vertical accuracy assessment of the WorldDEM™, the latest global DEM using the synthetic aperture radar interferometry (InSAR) method, based on the German TanDEM-X mission data. For reference data we use vertical profiles along the centerline of 47 paved runways located in different areas around the world. Our accuracy statement is based on the analysis of discrepancies between the reference data and the corresponding vertical profiles extracted from the WorldDEM™ dataset. Since the runways are nearly flat and have homogenous surfaces, the observed discrepancies are mainly due to instrument-induced error. Therefore, the derived accuracy statement has a universal character, e.g., it is not biased by other error sources including target- or environment-induced errors. Our main conclusions are that the WorldDEM™ is the most accurate global DEM to date in terms of its vertical accuracy; it appears that the accuracy is spatially independent.
Assessment of renal vasoconstriction in vivo after intra-arterial administration of the isosmotic contrast medium iodixanol compared to the low-osmotic contrast medium iopamidol.

BACKGROUND Low-osmotic contrast media (LOCM) such as iopamidol are known to increase the renal resistance index (RRI). The aim of our study was to evaluate in vivo the different effects of intra-arterial administration of LOCM in comparison to isosmotic contrast medium (IOCM) such as iodixanol on the human RRI. METHODS Twenty patients (16 males, 4 females; 66 years on average) with normal renal function (mean creatinine 1.0 mg/dl) had digital subtraction angiography (DSA) of the abdominal and lower-limb arteries. Ten patients received LOCM, and 10 patients IOCM (150 ml on average, 20 ml/s). The RRI was assessed by an experienced nephrologist with duplex ultrasound from 15 min before until 30 min after the first injection with delays of 1-5 min. The basic value of the RRI and differential RRI were calculated. RESULTS The basic value of the RRI was 0.69 in the LOCM group and 0.71 in the IOCM group. After LOCM a significant increase of the RRI to 0.73 on average (P < or = 0.001) 2 min after the first injection was found, whereas IOCM did not result in a significant change of the RRI (RRI remained 0.71 on average, P > or = 0.1). In the LOCM group, the RRI returned to the basic value after 30 min (+/-2.3 min). CONCLUSIONS Intra-arterial administration of IOCM had no influence on renal vascular resistance as expressed by the RRI, unlike LOCM, which induced a highly significant increase of the RRI for up to 30 min.
Reforms in Academic Publishing: Should Behavioral Disorders and Special Education Journals Embrace Them?

Bias poses a significant threat to the validity of research findings as well as practices and policies based on research. Reforms to academic publishing have been proposed and implemented in other fields to address bias in research. In this paper I review some sources of bias in research, some proposed areas of reform in academic publishing (e.g., disclosure, open data and methods, preregistration, methodological guidelines for reviewers, registered reports, open review), and some potential problems associated with the reforms (e.g., limited empirical support, additional time and effort associated with implementation, placing journals at a competitive disadvantage, researchers relinquishing control of their data). I conclude with some thoughts to frame decisions on whether and how Behavioral Disorders and other special education journals might adopt reforms to academic publishing.
Problematizing HRD in SMEs: A “Critical” Exploration of Context, Informality, and Empirical Realities

Small and medium-sized enterprises (SMEs) represent the backbone of the global economy and therefore are an integral part of the HRD research agenda. The HRD literature has predominantly focused on both large firms and formal practices, and as a consequence HRD in SMEs is considered deficient. In this article, we question these assumptions by invoking Mingers’ (2000) “four aspects of being critical” framework. We argue that the current knowledge base is flawed as research has not moved beyond the deficiency model to explore, accommodate, and explain HRD in the SME setting. The role of SME context and informality is insufficiently conceptualized in the literature. We make theoretical and methodological recommendations to advance HRD research.
Mortality Measurement and Modeling Beyond Age 100

The growing number of people living beyond age 100 emphasizes the need for accurate measurement and modeling of mortality at advanced ages. However, mortality measurement at extremely old ages poses serious challenges to researchers: age reporting at extreme ages may be inaccurate; small numbers of people at advanced ages requires pooling data for people belonging to different birthcohorts, which results in data heterogeneity; and, finally, a standard approach based on annual mortality estimates may not be applicable to extremely high and rapidly changing risk of death at advanced ages. The study uses data from the Social Security Administration Death Master File (DMF) to conduct mortality estimates for more homogeneous single-year birth cohorts with hazard rates estimated for narrow (monthly) age intervals. Mortality after age 88 was estimated for 1881-95 single-year extinct birth cohorts. Data quality control checks demonstrated that deceleration of mortality in later life is more expressed for data with lower quality. Additional quality checks using female-to-male ratio at advanced ages identified age 107 as the upper limit for acceptably good level of age reporting. Model comparison using Bayesian information criterion (BIC) showed that in the age interval 88 to 106 years and for data with reasonably good quality (U.S. Northern states), the Gompertz model shows better fitting of hazard rates than the logistic model. Hazard rate estimates obtained on the basis of DMF data agree well with estimates calculated on the basis of the 1900 actuarial cohort life table. This study shows that mortality deceleration in humans observed at advanced ages may be an artifact caused by age exaggeration, data heterogeneity or use of improper estimates of hazard rate. The phenomenon of mortality deceleration at older ages vanishes for datasets of higher data quality. The study was supported by National Institute on Aging Grant AG028620.
Characteristics of Borderline Personality Disorder: A Canadian Study

This study presents data on a Canadian sample of inpatients with the diagnosis of Borderline Personality Disorder (BPD). Inpatients with BPD were compared to inpatients with borderline traits. The results indicate that the BPD inpatients have a chronic severe disorder, which onsets in adolescence, and are likely to have suffered early deprivation or abuse.
Bone density of the femoral neck following Birmingham hip resurfacing

Background Resurfacing is a popular alternative to a standard hip replacement in young arthritic patients. Despite bone preservation around the femoral component, there is little information regarding the bone quality. Patients and methods 32 patients underwent consecutive Birmingham hip resurfacing. The bone density of the femoral neck was measured preoperatively and then at 6 weeks, 3 months, 1 year, and 2 years. The femoral neck was divided into regions of interest. Results were available for 27 hips in 26 patients. Results The overall femoral neck bone density showed a trend towards a decrease at 6 weeks and 3 months but returned to the preoperative level at 1 year, and was maintained at 2 years. The combined superior regions of the neck showed a statistically significant decrease in bone density at 6 weeks and 3 months. This returned to preoperative levels at 1 year and was maintained at 2 years. Interpretation Bone density appears to decrease at 6 weeks and 3 months, suggesting that care is necessary until bone density begins to recover.
Serial physical examinations, a simple and reliable tool for managing neonates at risk for early-onset sepsis

AIM To investigate whether serial physical examinations (SPEs) are a safe tool for managing neonates at risk for early-onset sepsis (EOS). METHODS This is a retrospective cohort study of neonates (≥ 34 wks’ gestation) delivered in three high-volume level IIIbirthing centres in Emilia-Romagna (Italy) during a 4-mo period (from September 1 to December 31, 2015). Neonates at risk for EOS were managed according to the SPEs strategy, these were carried out in turn by bedside nursing staff and physicians. A standardized form detailing general wellbeing, skin colour and vital signs was filled in and signed at standard intervals (at age 3, 6, 12, 18, 36 and 48 h) in neonates at risk for EOS. Three independent reviewers reviewed all charts of neonates and abstracted data (gestational age, mode of delivery, group B streptococcus status, risk factors for EOS, duration of intrapartum antibiotic prophylaxis, postpartum evaluations, therapies and outcome). Rates of sepsis workups, empirical antibiotics and outcome of neonates at-risk (or not) for EOS were evaluated. RESULTS There were 2092 live births and 1 culture-proven EOS (Haemophilus i) (incidence rates of 0.48/1000 live births). Most newborns with signs of illness (51 out of 101, that is 50.5%), and most of those who received postpartum antibiotics (17 out of 29, that is 58.6%) were not at risk for EOS. Compared to neonates at risk, neonates not at risk for EOS were less likely to have signs of illness (51 out of 1442 vs 40 out of 650, P = 0.009) or have a sepsis workup (25 out of 1442 vs 28 out of 650, P < 0.001). However, they were not less likely to receive empirical antibiotics (17 out of 1442 vs 12 out of 650, P = 0.3). Thirty-two neonates were exposed to intrapartum fever or chorioamnionitis: 62.5% (n = 20) had a sepsis workup and 21.9% (n = 7) were given empirical antibiotics. Among 216 neonates managed through the SPEs strategy, only 5.6% (n = 12) had subsequently a sepsis workup and only 1.9% (n = 4) were given empirical antibiotics. All neonates managed through SPEs had a normal outcome. Among 2092 neonates, only 1.6% (n = 34) received antibiotics; 1.4% (n = 29) were ill and 0.2% (n = 5) were asymptomatic (they were treated because of risk factors for EOS). CONCLUSION The SPEs strategy reduces unnecessary laboratory evaluations and antibiotics, and apparently does not worsen the outcome of neonates at-risk or neonates with mild, equivocal, transient symptoms.
Competing Loyalty Programs: Impact of Market Saturation, Market Share, and Category Expandability.

Abstract Loyalty programs have become an important component of firms' relationship management strategies. There are now some industries in which numerous rival loyalty programs are offered, inducing intense competition among these programs. However, existing research on loyalty programs has often studied such programs in a noncompetitive setting and has often focused on a single program in isolation. Addressing this gap, this research examines the effect of a firm's competitive positioning and market saturation on the performance of the firm's loyalty program. Based on the analysis of firm- and individual-level data from the airline industry, the results indicate that larger firms tend to benefit more from their loyalty program offerings than smaller firms. Moreover, when the product category demand is rigid, the impact of an individual loyalty program decreases as the marketplace becomes more saturated with competing programs. However, when the product category is highly expandable, the saturation effec.
[Monitoring of dairy cow claw health status in 15 herds using the computerised documentation program Claw Manager and digital parameters].

OBJECTIVE Monitoring of claw health over a defined period using the digital documentation and analysis program Claw Manager. MATERIAL AND METHODS Data from 679 cows were documented with the Claw Manager during routine functional claw trimming on 15 dairy farms that were visited two or three times. The data of these 33 visits were analysed for the following parameters: prevalence of claw lesions, of their severity scores and of lameness as well as the Cow Claw Score (CCS), the Farm Claw Score (FCS) and the Farm Zone Score (FZS). Their chronological progression was shown using boxplot graphs. RESULTS Mean prevalence of all lame free cows was 71.9% at visit 1 (max. 95.0%, min. 21.1%) and 72.9% at visit 2 (max. 100.0%, min. 12.6%). The mean prevalence of claw lesions in all 15 herds was 61.8% for heel horn erosion (HHE), followed by white line lesions (WLL, 37.2%), sole haemorrhages (SH, 27.5%), acute and chronic stages of digital dermatitis (DD, 19.7%) and chronic laminitic claws (10.9%). In individual herds HHE (n = 15), WLL (n = 11), SH (n = 10), acute DD (n = 4) and chronic laminitic claws (n = 3) were consistently among the three most frequently observed lesions. A statistically significant improvement was found for the severity scores of the claw lesions of all cows from visit 1 to visit 2. The CCS ranged from 0 (CCS min) to 276 (CCS max), the FCS ranged from 6 to 72. The length of the upper quartiles and the length of the upper whiskers in the boxplot graphs of the CCS values of the herds at the various visits varied widely. The CCS of the cows of ten herds improved significantly from visit 1 to visit 2. Locomotion scores and CCS were significantly correlated on 30 of 33 visits. CONCLUSION The parameters FCS (median of all CCS values of a herd), length of the upper quartiles, length of the upper whiskers in the boxplot graphs FZS max, the prevalence of lameness and of claw lesions, and their severity scores proved to be very informative for a detailed comparison of claw data of herds over subsequent visits.
Influence of moderate to severe chronic periodontitis on dental pulp

Background: The relationship between periodontal disease and dental pulp changes is controversial and has been debated for many years. This human study was performed to evaluate the possible effects of moderate to advanced periodontal disease on the different aspect of dental pulp structure. Materials and Methods: Twenty hopeless permanent teeth were extracted from systemically healthy adults because of moderate to advanced chronic periodontitis, with a bone loss of >6 mm and a mobility of grade 2 or 3. Upon extraction, the apical 2 to 3 mm of the roots were immediately sectioned. Four to five sections were mounted on each slide, and every third slide was stained with hematoxylin and eosin. The specimens were histologically processed and examined by an oral pathologist. Results: Non-inflamed pulp, with partial or complete necrosis in some sections and several non-necrotic sections, was found in only 6.3% of teeth. Most teeth (58.3%) displayed edematous pulps. Slightly fibrotic pulps were seen in 52.1% of sections. Odontoblastic integrity was seen in 31.3% of teeth. Most teeth (77.1%) displayed no pulp stones. In 43.8% of teeth, the pulp vessels displayed dilatation. Conclusions: Moderate to advanced periodontal disease can affect the dental pulp. Careful consideration of diagnostic and treatment planing in patients with endodontic-periodontal involvement is therefore recommended.