Miracle-dz/UniFAR-FTUs huggingface dataset:
Smoking increases the risk of relapse after successful tuberculosis treatment

Background Recent tobacco smoking has been identified as a risk factor for developing tuberculosis, and two studies which have investigated its association with relapse of tuberculosis after completion of treatment had conflicting results (and did not control for confounding). The objective of this study was to investigate risk factors for tuberculosis relapse, with emphasis on smoking. Methods A cohort of newly diagnosed TB cases was followed up from their discharge after completion of treatment (in 2001–2003) until October 2006 and relapses of tuberculosis ascertained during that period. A case of relapse was defined as a patient who started a second treatment during the follow up. Results Smoking (OR 2.53, 95% CI 1.23–5.21) and living in an area where the family health program was not implemented (OR 3.61, 95% CI 1.46–8.93) were found to be independently associated with relapse of tuberculosis. Conclusions Our results establish that smoking is associated with relapse of tuberculosis even after adjustment for the socioeconomic variables. Smoking cessation support should be incorporated in the strategies to improve effectiveness of Tuberculosis Control Programs.
Intrapartum PCR assay versus antepartum culture for assessment of vaginal carriage of group B streptococci in a Danish cohort at birth

The aim of this study was to compare the performances of two strategies for predicting intrapartum vaginal carriage of group B streptococci (GBS). One strategy was based on an antepartum culture and the other on an intrapartum polymerase chain reaction (PCR). We conducted a prospective observational study enrolling 902 pregnant women offered GBS screening before delivery by two strategies. The Culture-strategy was based on vaginal and rectal cultures at 35–37 weeks’ gestation, whereas the PCR-strategy was based on PCR assay on intrapartum vaginal swab samples. An intrapartum vaginal culture for GBS was used as the reference standard from which the performances of the 2 strategies were evaluated. The reference standard showed a GBS-prevalence of 12%. The culture-strategy performed with a sensitivity of 82%, specificity of 91%, positive predictive value (PPV) of 55%, negative predictive value (NPV) of 98%, and Likelihood ratio (LH+) of 9.2. The PCR-strategy showed corresponding values as sensitivity of 83%, specificity of 97%, PPV of 78%, NPV of 98%, and LH+ of 27.5. We conclude that in a Danish population with a low rate of early-onset neonatal infection with GBS, the intrapartum PCR assay performs better than the antepartum culture for identification of GBS vaginal carriers during labor.
Multi-proxy Characterization of Hurricanes Rita and Ike Storm Deposits in the Rockefeller Wildlife Refuge, Southwestern Louisiana

ABSTRACT Yao, Q. ; Liu, K. -B. , and Ryu, J., 2018. Multi-proxy Characterization of Hurricane Rita and Ike Storm Deposits in a Coastal Marsh in the Rockefeller Wildlife Refuge, Southwestern Louisiana. In: Shim, J.-S. ; Chun, I. , and Lim, H.S. (eds.), Proceedings from the International Coastal Symposium (ICS) 2018 (Busan, Republic of Korea). Journal of Coastal Research, Special Issue No. 85, pp. 841–845. Coconut Creek (Florida), ISSN 0749-0208. In 2005 and 2008, Hurricanes Rita and Ike made landfalls as category 3 and 2 hurricanes to the west of Rockefeller Wildlife Refuge (RWR) in southwestern Louisiana. In 2013, three ~30 cm sediment monoliths dominated by brown clay were recovered along a ~30 m transect perpendicular to the shoreline from the RWR. Each monolith contains two distinct light-colored calcareous storm deposits that are attributable to these two landfalling hurricanes. Loss-onignition and X-ray fluorescence (XRF) analyses were performed on all three sediment monoliths to study the sedimentological and geochemical characteristics of these two storm deposits. The geochemical results show that the storm deposits are characterized by higher-than-average values of Ca, Sr, Zr, and carbonates and low percentages of water and organics. In addition, remote sensing images show that the rate of average shoreline retreat at the RWR is ~14.5 m/yr from 1998 to 2017, and 19 m/year and 25.5 m/yr during the Hurricane Rita and Ike years, respectively. Both loss-on-ignition and XRF results also show that despite being a stronger storm, the Hurricane Rita layers are much thinner than those of Hurricane Ike in all monoliths. Remote sensing data support our interpretation that Hurricane Rita caused significant shoreline erosion and coastal recession in 2005, rendering the sampling locations at least 30 m closer to the ocean and thereby more susceptible to storm surges when Hurricane Ike struck in 2008. Thus, these results suggest that site-to-sea distance is an important factor in determining the thicknesses of storm deposits in coastal wetlands, particularly along shorelines undergoing rapid marine transgression.
Anchor Selection Strategies for DIF Analysis

Differential item functioning (DIF) indicates the violation of the invariance assumption, for instance, in models based on item response theory (IRT). For item-wise DIF analysis using IRT, a common metric for the item parameters of the groups that are to be compared (e.g., for the reference and the focal group) is necessary. In the Rasch model, therefore, the same linear restriction is imposed in both groups. Items in the restriction are termed the ``anchor items''. Ideally, these items are DIF-free to avoid artificially augmented false alarm rates. However, the question how DIF-free anchor items are selected appropriately is still a major challenge. Furthermore, various authors point out the lack of new anchor selection strategies and the lack of a comprehensive study especially for dichotomous IRT models. This article reviews existing anchor selection strategies that do not require any knowledge prior to DIF analysis, offers a straightforward notation, and proposes three new anchor selection strategies. An extensive simulation study is conducted to compare the performance of the anchor selection strategies. The results show that an appropriate anchor selection is crucial for suitable item-wise DIF analysis. The newly suggested anchor selection strategies outperform the existing strategies and can reliably locate a suitable anchor when the sample sizes are large enough.
Primates Face to Face

Foreword Karen Strier Introduction Agustin Fuentes and Linda D. Wolfe Part I. Science and Nonhuman Primates: 1. Anthropology and Primatology Phyllis Dolhinow 2. Resistance to the cross-species perspective in anthropology Mary M. Pavelka 3. The ethics and efficacy of biomedical research in Chimpanzees with special regard to HIV research Roger S. Fouts, Deborah H. Fouts and Gabriel S. Waters Part II. Cultural Views of Nonhuman Primates: 4. Introduction to section Agustin Fuentes and Linda D. Wolfe 5. Monkey as food, monkey as child: Guaja symbolic cannibalism Loretta A. Cormier 6. Ethnoecology of monkeys among the Bari of Venezuela: perception, use and conservation Manuel Lizzaralde 7. Primates in Matsigenka subsistence and world view Glenn Shepard 8. Monkey King in China: basis for a conservation policy Frances Burton 9. Local population, conservation efforts and the mountain gorillas of Rwanda Pascale Sicotte and Prosper Uwengeri Part III. Conservation of Nonhuman Primates: 10. Introduction to section Agustin Fuentes and Linda Wolfe 11. Monkeys, humans and politics in the Mentawai Islands: no simple solutions in a complex world Augustin Fuentes 12. Conservation must pursue a human-nature biosynergy in the era of social chaos and bushmeat commerce Anthony L. Rose 13. A cultural primatological study of Macaca fascicularis on Ngeaur Island, Republic of Palau Bruce Wheatley, Rebecca Stephenson, Hiro Kurashina and Kelly Kautz 14. Monkeys in the back yard: encroaching wildlife and rural communities in Japan David Sprague Part IV. Local Economics: Goverment Actions and Nonhuman Primates: 15. Introduction to section Agustin Fuentes and Linda Wolfe 16. The primatologist as minority advocate Ardith Eudey 17. Monkey Business? The conservation implications of macaque ethnoprimatology in southern Thailand Lesley E. Sponsel, Nukul Ruttanadakul and Poranee Natadecha-Sponsel 18. Rhesus macaques: a comparative study of two sites, Jaipur, India and Silver Springs, Florida Linda Wolfe.
Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study

The human Y is a genetically degenerate chromosome, which has lost about 97% of the genes originally present. Most of the remaining human Y genes are in large duplicated segments (ampliconic regions) undergoing intense Y–Y gene conversion. It has been suggested that Y–Y gene conversion may help these genes getting rid of deleterious mutations that would inactivate them otherwise. Here, we tested this idea by simulating the evolution of degenerating Y chromosomes with or without gene conversion using the most up-to-date population genetics parameters for humans. We followed the fate of a variant with Y–Y gene conversion in a population of Y chromosomes where Y–Y gene conversion is originally absent. We found that this variant gets fixed more frequently than the neutral expectation, which supports the idea that gene conversion is beneficial for a degenerating Y chromosome. Interestingly, a very high rate of gene conversion is needed for an effect of gene conversion to be observed. This suggests that high levels of Y-Y gene conversion observed in humans may have been selected to oppose the Y degeneration. We also studied with a similar approach the evolution of ampliconic regions on the Y chromosomes and found that the fixation of many copies at once is unlikely, which suggest these regions probably evolved gradually unless selection for increased dosage favored large-scale duplication events. Exploring the parameter space showed that Y–Y gene conversion may be beneficial in most mammalian species, which is consistent with recent data in chimpanzees and mice.
Echocardiographic parameters are independently associated with increased cardiovascular events in patients with chronic kidney disease.

BACKGROUND Patients with chronic kidney disease (CKD) are associated with increased cardiovascular (CV) morbidity and mortality. Echocardiographic measures of heart structure and function have been reported to predict adverse CV outcomes in various pathologic conditions. The aim of this study is to assess whether echocardiographic parameters are independently associated with increased CV events in patients with CKD Stages 3-5. METHODS We consecutively enrolled 505 CKD patients from our outpatient department of internal medicine. CV events were defined as CV death, hospitalization for unstable angina, non-fatal myocardial infarction, sustained ventricular arrhythmia, hospitalization for congestive heart failure, transient ischemia attack and stroke. The relative CV events' risk was analyzed by Cox regression methods. RESULTS In the multivariate analysis, old age, the presence of diabetes, coronary artery disease and atrial fibrillation; decreased serum albumin and hematocrit levels; left atrial diameter (LAD) >4.7 cm [hazard ratio (HR), 2.141; 95% confidence interval (CI), 1.155-3.971, P = 0.016]; increased left ventricular mass index (LVMI) (HR, 1.006; 95% CI, 1.002 to 1.010, P = 0.003) and left ventricular ejection fraction (LVEF) <55% (HR, 2.007; 95% CI, 1.007-3.743, P = 0.028) were independently associated with increased CV events. CONCLUSIONS Our findings show that LAD >4.7 cm, increased LVMI and LVEF <55% are independently associated with adverse CV outcomes in CKD patients. Screening CKD patients by means of echocardiography may help identify a high-risk group of poor CV prognosis.
SMASH: a tool for articulatory data processing and analysis

Recent innovations in 3D motion capture technology such as electromagnetic articulography (EMA) are providing unprecedented access to the intricate movements of the articulators during speech production. Although these technological advances afford exciting opportunities for advancing the assessment and treatment of speech, they have presented new challenges associated with data collection, processing, and analysis. To address these challenges, we have standardized our EMA data collection protocols and developed a Matlab-based software tool, SMASH, for processing, visualizing, and analyzing speech movement data. The goal of the software is to advance research on speech production by improving the efficiency and reliability of speech movement analyses.
Impact of strained-silicon-on-insulator (sSOI) substrate on FinFET mobility

In this letter, it is shown that for fin widths down to < 20 nm, strain can be retained in patterned strained-silicon-on-insulator (sSOI) films and is correlated to mobility enhancements observed in FinFET devices. NMOS FinFET mobility is improved by 60% and 30% for [110]/<110> and (100)/<100> fin surface/direction, respectively. Although PMOS FinFET mobility is degraded by 35% for [110]/<110> fins, it is enhanced by up to 30% for (100)/<100> fins. These results can be qualitatively explained using the bulk-Si piezoresistance coefficients.
Human Autoantibody Silencing by Immunoglobulin Light Chains

Several newly arising human antibodies are polyreactive, but in normal individuals the majority of these potentially autodestructive antibodies are removed from the repertoire by receptor editing or B cell deletion in the bone marrow. To determine what proportion of naturally arising autoantibodies can be silenced by immunoglobulin (Ig) light chain receptor editing, we replaced the light chains in 12 such antibodies with a panel of representative Igκ and Igλ chains. We found that most naturally arising autoantibodies are readily silenced by light chain exchange. Thus, receptor editing may account for most autoreactive antibody silencing in humans. Light chain complementarity determining region (CDR) isoelectric points did not correlate with silencing activity, but Igλ genes were more effective than Igκ genes as silencers. The greater efficacy of Igλ chains as silencer of autoreactivity provides a possible explanation for the expansion and altered configuration of the Igλ locus in evolution.
Impairment of high‐contrast visual acuity in Parkinson's disease

Several studies have shown that the visual system is affected in Parkinson's disease (PD) with reduced contrast sensitivity, low‐contrast acuity, and flicker sensitivity, as well as altered electroretinograms (ERGs) and pattern visual evoked potentials (VEPs). Apparently, however, no study has yet specifically determined whether visual acuity to high‐contrast stimuli is impaired in PD. Visual acuity was measured in a group of 16 patients with PD, both on and off drugs (for 24 h), and 16 age‐ and sex‐matched normal control subjects. Acuity was impaired in the PD group both on standard Snellen chart and on a screen in a computerized test of visual resolution. The degree of impairment was 24 and 25%, respectively, in the two tests. The PD patients had marginally better acuity on both tests while receiving drugs, but the differences were not significant. The difference between the two groups was consistent with impaired resolution and could not be accounted for by any perceptual dysfunction that may also have been present in the PD group. Conversely, however, impaired acuity may be implicated in studies that have reported mild deficits of visuospatial/visuoperceptual function in PD. Reduced acuity appears to be a subtle sequela of dopaminergic deficiency in the visual system.
Adult age and the speed-accuracy trade-off.

Three experiments were conducted to investigate the possibility that previously reported age differences in speed of performance were caused by older subjects placing more emphasis on accuracy than younger subjects. The speculation that older subjects generally have a greater emphasis on accuracy was confirmed, but only in one of the experiments was the complete age difference in speed found to be attributable to an age difference in accuracy. It was concluded that although a speed-accuracy trade-off cannot account for all age differences in speed, the greater bias towards accuracy in older subjects and the problems associated with interpreting traditional reaction time make it advisable that future researchers in this area employ procedures that allow an empirical determination of the relationship between speed and accuracy.
Does iron overload really matter in stem cell transplantation?

A growing body of evidence suggests that iron overload is associated with inferior outcomes after myeloablative allogeneic hematopoietic stem cell transplantation (HSCT). However, all of those studies used surrogate markers of iron overload, especially serum ferritin, and most had a retrospective design. We conducted a prospective observational study in patients with myelodysplastic syndrome or acute leukemia undergoing myeloablative HSCT. Forty‐five patients who were followed for over 1 year, with serial measurements of serum iron parameters, as well as liver and cardiac magnetic resonance imaging. There was no significant increase in ferritin, liver or cardiac iron content in the 12 months following HSCT. Although serum ferritin still appeared to have prognostic significance, as previously reported, pre‐HSCT iron overload (as reflected in liver iron content) was not associated with increased mortality, relapse, or graft‐versus‐host disease. These results raise the possibility that the adverse prognostic impact of pre‐HSCT hyperferritinemia may be related to factors independent of iron overload. Am. J. Hematol. 87:569–572, 2012. © 2012 Wiley Periodicals, Inc.
Heritability of complex white matter diffusion traits assessed in a population isolate

Diffusion weighted imaging (DWI) methods can noninvasively ascertain cerebral microstructure by examining pattern and directions of water diffusion in the brain. We calculated heritability for DWI parameters in cerebral white (WM) and gray matter (GM) to study the genetic contribution to the diffusion signals across tissue boundaries.
Absolute Reduction in Lower Limb Lean Body Mass in Japanese Women With Knee Osteoarthritis

Background:Knee osteoarthritis (OA) is a significant contributor to disability, and obesity is one of the most modifiable risk factors. The association between knee OA and obesity has been reported to relate to quadriceps strength. To begin to examine this hypothesis, independent measures of quadriceps lean mass are needed. Objective:The objective of this study was to characterize the absolute lower limb lean body mass in women with knee OA. Methods:Japanese women, aged 45 and over, who presented to a community orthopedics clinic, were categorized as 1) those with no knee pain, presenting with fracture, sprain, or back pain (n = 604); and 2) those presenting with knee pain meeting clinical and radiographic criteria for knee OA (n = 341). Segmental lower limb lean body mass (L-LBM) was measured with multifrequency bioelectrical impedance analysis and subjects were stratified by body mass index (BMI) by Western Pacific Region World Health Organization weight categories. Results:Control and knee OA groups were comparable with respect to age and BMI. Despite an increase in L-LBM with increasing BMI, there was a statistically significant reduction in L-LBM in knee OA subjects in comparison with control subjects in matched normal weight, overweight, and obese strata (11.1, 12.4, and 13.1 kg in the nonknee OA compared with 10.5, 10.6, and 11.6 kg in the knee OA group). Conclusions:A reduction in absolute L-LBM is observed in older Japanese women with knee OA in comparison with control subjects. Longitudinal studies are warranted in which L-LBM can be prospectively evaluated in a cohort followed for incident knee OA to better characterize the temporal relationship with L-LBM decline. Clinicians should consider this reduction in L-LBM in women with knee OA to recommend therapy aimed at reducing risk for atrophy and disability.
New Haven survey of joint diseases. XII. Distribution and symptoms of osteoarthrosis in the hands with reference to handedness.

It has been known for many years that osteoarthrosis can be caused by trauma. More recently however, the concept, first developed by Kellgren and Moore (1952), that osteoarthrosis may in some instances involve many joints in the body and have a systemic basis, has gained acceptance. This condition is known as either generalized or primary osteoarthrosis, and the degenerative disease of an isolated joint is known as traumatic or secondary osteoarthrosis (Kellgren, 1961, 1964). In this paper a detailed analysis is presented of the patterns and symptoms of osteoarthrosis in the hands of a population sample living in a town on the East Coast of the United States. The results indicate that there may be a traumatic element in generalized osteoarthrosis.
Pharmacological Targeting of Glucagon and Glucagon-Like Peptide 1 Receptors Has Different Effects on Energy State and Glucose Homeostasis in Diet-Induced Obese Mice

Pharmacologic contributions of directly agonizing glucagon-like peptide 1 (GLP-1) receptor or antagonizing glucagon receptor (GCGR) on energy state and glucose homeostasis were assessed in diet-induced obese (DIO) mice. Metabolic rate and respiratory quotient (RQ), hyperglycemic clamp, stable isotope-based dynamic metabolic profiling (SiDMAP) studies of 13C-labeled glucose during glucose tolerance test (GTT) and gene expression were assessed in cohorts of DIO mice after a single administration of GLP-1 analog [GLP-1-(23)] or anti-GCGR antibody (Ab). GLP-1-(23) and GCGR Ab similarly improved GTT. GLP-1-(23) decreased food intake and body weight trended lower. GCGR Ab modestly decreased food intake without significant effect on body weight. GLP-1-(23) and GCGR Ab decreased RQ with GLP-1, causing a greater effect. In a hyperglycemic clamp, GLP-1-(23) reduced hepatic glucose production (HGP), increased glucose infusion rate (GIR), increased glucose uptake in brown adipose tissue, and increased whole-body glucose turnover, glycolysis, and rate of glycogen synthesis. GCGR Ab slightly decreased HGP, increased GIR, and increased glucose uptake in the heart. SiDMAP showed that GLP-1-(23) and GCGR Ab increased 13C lactate labeling from glucose, indicating that liver, muscle, and other organs were involved in the rapid disposal of glucose from plasma. GCGR Ab and GLP-1-(23) caused different changes in mRNA expression levels of glucose- and lipid metabolism-associated genes. The effect of GLP-1-(23) on energy state and glucose homeostasis was greater than GCGR Ab. Although GCGR antagonism is associated with increased circulating levels of GLP-1, most GLP-1-(23)-associated pharmacologic effects are more pronounced than GCGR Ab.