Miracle-dz/UniFAR-FTUs huggingface dataset:
Interpreting Tuberculin Skin Tests in a Population With a High Prevalence of HIV, Tuberculosis, and Nonspecific Tuberculin Sensitivity

Understanding the epidemiology and clinical course of tuberculosis is hampered by the absence of a perfect test for latent tuberculosis infection. The tuberculin skin test (TST) is widely used but suffers poor specificity in those receiving the bacille Calmette-Guérin vaccine and poor sensitivity in individuals with human immunodeficiency virus (HIV) infections. TST responses for a target population in Harare, Zimbabwe (HIV prevalence, 21%), recruited in 2005–2006, were interpreted by using a separate calibration population in Harare, for which interferon-gamma release assays (enzyme-linked immunosorbent spot (ELISpot)) results were also known. Statistical fitting of the responses in the calibration population allowed computation of the probability that an individual in the target population with a given TST and HIV result would have tested ELISpot positive. From this, estimates of the prevalence of tuberculosis infection, and optimal TST cutpoints to minimize misdiagnosis, were computed for different assumptions about ELISpot performance. Different assumptions about the sensitivity and specificity of ELISpot gave a 40%–57% prevalence of tuberculosis infection in the target population (including HIV-infected individuals) and optimal TST cutpoints typically in the 10 mm–20 mm range. However, the optimal cutpoint for HIV-infected individuals was consistently 0 mm. This calibration method may provide a valuable tool for interpreting TST results in other populations.
Round-Robin Scheduling for Orthogonal Beamforming with Limited Feedback

We propose a round-robin scheduling algorithm for orthogonal beamforming with a strict signal to interference-plus-noise ratio (SINR) constraint and limited feedback. The presented algorithm aims at scheduling the users at identical slots over different blocks, in order to reduce the necessary scheduling overhead, and to minimize the maximum delay between serving the same user. Thus, the presented algorithm is especially suited for real-time multimedia traffic. The algorithm allocates the users using orthogonal beamforming based on the quantized feedback provided by the users. The quantized feedback consists of the estimated power that is necessary to fulfill a predefined SINR constraint. Further, we propose an algorithm to design codebooks to quantize the estimated power. Using the feedback, the base station redistributes power from users with spare power to users that lack power so that they fulfill their SINR constraints. The performance of the algorithm is demonstrated through simulations.
Are lemming winter nest counts a good index of population density?

Abstract Lemmings construct nests of grass and moss under the snow during winter, and counting these nests in spring is 1 method of obtaining an index of winter density and habitat use. We counted winter nests after snow melt on fixed grids on 5 areas scattered across the Canadian Arctic and compared these nest counts to population density estimated by mark–recapture on the same areas in spring and during the previous autumn. Collared lemmings were a common species in most areas, some sites had an abundance of brown lemmings, and only 2 sites had tundra voles. Winter nest counts were correlated with lemming densities estimated in the following spring (rs = 0.80, P < 0.001), but less well correlated with densities the previous autumn (rs = 0.55, P < 0.001). Winter nest counts can be used to predict spring lemming densities with a log-log regression that explains 64% of the observed variation. Winter nest counts are best treated as an approximate index and should not be used when precise, quantitative lemming density estimates are required. Nest counts also can be used to provide general information about habitat-use in winter, predation rates by weasels, and the extent of winter breeding.
Subtype-Specific Selection for Resistance to Fluoroquinolones but Not to Tetracyclines Is Evident in Campylobacter jejuni Isolates from Beef Cattle in Confined Feeding Operations in Southern Alberta, Canada

ABSTRACT Campylobacter jejuni was longitudinally isolated from beef cattle housed in four confined feeding operations (CFOs) in Southern Alberta, Canada, over 18 months. All of the cattle were administered a variety of antimicrobial agents (AMAs) nontherapeutically and metaphylactically during their time in the CFOs. In total, 7,966 C. jejuni isolates were recovered from cattle. More animals were colonized by the bacterium after >60 days in the CFO (interim) than were individuals upon entry at the CFO (arrival). Subtyping and resistance to seven AMAs were determined for 1,832 (23.0%) and 1,648 (20.7%) isolates, respectively. Increases in the proportion of isolates resistant to tetracycline were observed at all four CFOs between sample times and to ciprofloxacin and nalidixic acid at one or more CFOs. The vast majority of isolates resistant to tetracycline carried tetO, whereas ciprofloxacin resistance was predominantly attributed to mutations in the gyrA gene. Although considerable diversity was observed, a majority of C. jejuni isolates belonged to one of five predominant subtype clusters. There was no difference in subtype diversity by CFO, but the population structure differed between sample times. Selection for resistance to ciprofloxacin and nalidixic acid was subtype dependent, whereas selection for resistance to tetracycline was not. The findings indicate that a proportion of cattle entering CFOs carry resistant C. jejuni subtypes, and the characteristics of beef cattle CFOs facilitate transmission/proliferation of diverse subtypes, including those resistant to AMAs, which coupled with the densities of CFOs likely contribute to the high rates of cattle-associated campylobacteriosis in Southern Alberta. IMPORTANCE A small proportion of cattle entering a CFO carry Campylobacter jejuni, including subtypes resistant to AMAs. The large numbers of cattle arriving from diverse locations at the CFOs and intermingling within the CFOs over time, coupled with the high-density housing of animals, the high rates of transmission of C. jejuni subtypes among animals, and the extensive use of AMAs merge to create an ideal situation where the proliferation of diverse antimicrobial-resistant C. jejuni subtypes is facilitated. Considering that Southern Alberta reports high rates of campylobacteriosis in the human population and that many of these clinical cases are due to C. jejuni subtypes associated with cattle, it is likely that the characteristics of beef cattle CFOs favor the propagation of clinically relevant C. jejuni subtypes, including those resistant to medically important AMAs, which constitute a risk to human health.
The Autistic Spectrum Disorders

Autism has long been the paradigmatic syndrome for a group of conditions most recently classified in theDiagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) under the category of Pervasive Developmental Disorders. However, more recent considerations of this group of conditions suggest that a spectrum of symptoms more accurately reflects the nature of these disorders, leading to the current concept of Autism Spectrum Disorders (ASDs). Autism and the ASDs come from a long history of confusion and stigma. Even before the syndrome was originally named by Leo Kanner in his 1943 paper, as a condition of “autistic disturbance of affective contact,” the condition has been the focus of considerable confusion. Some of this confusion comes from the association of the term “autism” with the so-called “4 A’s” that Eugen Bleuler used to characterize schizophrenia. This was compounded by descriptions of Victor, the Wild Boy of Aveyron who, after allegedly having been reared by wolves, was brought to Paris and trained by the French psychologist Itard. And, with the advent of the psychoanalytic era of psychiatric theories, Bettelheim’s Empty Fortress and Margaret Mahler’s “normal autistic phase” of development suggested that failures in parenting caused this pervasive and persistent disorder. This early work gave rise to notions about “refrigerator” mothers as the cause of such serious psychopathology and created an enormous burden and stigma for parents seeking to understand and care for their children. Sadly, some of these biases and misconceptions persist to this day, interfering with early diagnosis and treatment as well as scientific approaches to research on autism. Today we understand ASDs to be a group of clinical syndromes that have varying degrees of two fundamental elements: developmental delays and developmental deviations. Two-thirds of cases have evidence of atypical development before 12 months, and one-third of cases have a regression in speech and language before 18 months. Onset occurs before 30 months for all but childhood disintegrative disorder. The core syndrome includes deficits in social interactions and communication, along with presence of stereotyped behaviors, activities, and interests. The prototypic ASD is autistic disorder. The other ASDs, including Rett’s disorder, childhood disintegrative disorder, Asperger’s disorder, and pervasive developmental disorder not otherwise specified (PDD NOS), share many of the core features of autistic disorder.
Limb remote ischemic post-conditioning reduces injury and improves long-term behavioral recovery in rats following subarachnoid hemorrhage: Possible involvement of the autophagic process

Hemorrhage-related neurologic injury is a primary cause of disability and mortality following subarachnoid hemorrhage (SAH). The aim of the present study was to investigate the potential neuroprotective effect and the possible role of autophagy in limb remote ischemic post-conditioning (RIPostC) using an endovascular puncture rat model of SAH. RIPostC was induced by three cycles of occlusion (10 min) and release (10 min) in the bilateral femoral artery using an aneurysm clip. Early RIPostC began immediately following SAH, delayed RIPostC began following a 30 min delay and the repeated RIPostC group underwent the protocol every day for 3 days. Brain water content, SAH grading, terminal deoxynucleotidyl transferase dUTP nick end labeling-DAPI staining, transmission electron microscopy, and neurological and behavioral tests were conducted three days following surgery. Long term outcomes of behavior and memory were assessed using a rotarod test and Morris water maze test 1 month subsequently. Biomarkers of autophagy, including Beclin-1 and light chain 3 (LC3), were assessed using western blotting. The results of the present study demonstrated that, compared with other groups, repeated RIPostC was able to alleviate brain edema, prevent neuronal apoptosis, and improve short term and long term neurological function and memory. Beclin-1 and LC3 in the cortex were upregulated following treatment with repeated RIPostC. Autolysosomes increased 3 days following SAH and were maintained for 1 month in the repeated RIPostC group. Therefore, the present study indicated that the optimized repeated RIPostC may provide a noninvasive strategy to induce neuroprotection, and improve the short and long term outcomes of SAH-related cerebral injury, possibly involving the autophagy pathway.
The Near-Eastern Roots of the Neolithic in South Asia

The Fertile Crescent in the Near East is one of the independent origins of the Neolithic, the source from which farming and pottery-making spread across Europe from 9,000 to 6,000 years ago at an average rate of about 1 km/yr. There is also strong evidence for causal connections between the Near-Eastern Neolithic and that further east, up to the Indus Valley. The Neolithic in South Asia has been far less explored than its European counterpart, especially in terms of absolute (14C) dating; hence, there were no previous attempts to assess quantitatively its spread in Asia. We combine the available 14C data with the archaeological evidence for early Neolithic sites in South Asia to analyze the spatio-temporal continuity of the Neolithic dispersal from the Near East through the Middle East and to the Indian subcontinent. We reveal an approximately linear dependence between the age and the geodesic distance from the Near East, suggesting a systematic (but not necessarily uniform) spread at an average speed of about 0.65 km/yr.
Fungi diversity in PM 2. 5 and PM 1 at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

Abstract. Fungi are ubiquitous throughout the near-surface atmosphere, where they represent an important component of primary biological aerosol particles. This study combined internal transcribed spacer region sequencing and quantitative real-time polymerase chain reaction (qPCR) to investigate the ambient fungi in fine (PM2. 5, 50 % cutoff aerodynamic diameter Da50 = 2.5 µm, geometric standard deviation of collection efficiency σg = 1.2) and submicron (PM1, Da50 = 1 µm, σg = 1.2) particles at the summit of Mt. Tai located in the North China Plain, China. Fungal abundance values were 9.4 × 104 and 1.3 × 105 copies m−3 in PM2. 5 and PM1, respectively. Most of the fungal sequences were from Ascomycota and Basidiomycota, which are known to actively discharge spores into the atmosphere. The fungal community showed a significant seasonal shift across different size fractions according to Metastats analysis and the Kruskal–Wallis rank sum test. The abundance of Glomerella and Zasmidium increased in larger particles in autumn, whereas Penicillium, Bullera, and Phaeosphaeria increased in smaller particles in winter. Environmental factors, namely Ca2+, humidity, and temperature, were found to be crucial for the seasonal variation in the fungal community. This study might serve as an important reference for fungal contribution to primary biological aerosol particles.
Perceptions of equity and justice and their implications on affective organizational commitment: a confirmatory study in a teaching and research institute

Studies about individuals commitment to organizations acquire renewed interest in light of the changes imposed by new organizational structures and 'boundary-less' careers. The need to identify and retain individuals who add value to the organization constitutes an increasing challenge facing human resource professionals. In this context it is necessary to establish stronger links between the individuals and the organization they work for. In this paper the effects of the perceived equity and justice on the employees' affective commitment to the organization is evaluated, using a structural equation model. The main stream of the literature treats equity as part of distributive justice. The main contribution of this study was to treat both concepts separately. Based on data gathered from a teaching and research institute, this study confirmed the theoretical assumptions that the perception of justice is indeed antecedent to and determinant of affective organizational commitment. However, the same was not observed in relation to the perception of equity. This result justifies the new approach of removing the concept of equity from justice when measuring organizational commitment.
Taxonomic utility of achene morphology and anatomy in Anemone L. (Ranunculaceae) species

Achene macroand micromorphology and pericarp anatomy are described in four Polish species of Anemone (A. narcissiflora, A. nemorosa, A. ranunculoides, A. sylvestris). Biometric analysis showed that achene size varies greatly in all the studied species and is of limited diagnostic value. Three types of sculpture connected with the character of the indumentum were distinguished. The presence or absence of stomata on the achene style and the character of the hair base differentiated A. nemorosa and A. ranunculoides, which have the same type of pericarp ornamentation. The endocarp (number of layers and outline of its cells) was shown to be useful in the systematics of Anemone.
Laparoscopic Cholecystectomy Under Low Thoracic Combined Spinal Epidural Anaesthesia: A Comparative Study Between Isobaric And Hyperbaric Bupivacaine

Background: Thoracic spinal anaesthesia has proven its efficacy over general anaesthesia as a routine anaesthetic technique for laparoscopic surgeries. This study aimed to compare the block characteristics of isobaric and hyperbaric bupivacaine in thoracic spinal epidural anaesthesia for laparoscopic cholecystectomies. Materials and methods: The study included 60 ASA I and II patients undergoing elective laparoscopic cholecystectomy, divided randomly into two equal groups. Both the groups were given thoracic combined spinal epidural anaesthesia (CSE) at the T9-T10 / T10-T11 interspace using 1.5 ml of isobaric bupivacaine 0.5% (5 mg/ml) + 25μg (0.5 ml) of fentanyl in group I and 1.5 ml of hyperbaric bupivacaine 0.5% (5 mg/ml) + 25μg (0.5 ml) of fentanyl in group H. Results: The onset of analgesia was comparable in both the groups. In contrast to the longer time taken to reach T4(7.8 min) by hyperbaric bupivacaine which also showed longer motor(220min) than sensory block(117min); isobaric bupivacaine showed lesser time to reach T4(2min) and a shorter duration of motor block (90 min) than the sensory block(160min). Conclusion: By providing a sensory block of longer duration than the motor block isobaric bupivacaine is reflected in a better indication for upper abdominal laparoscopic surgeries.
Spray Formation during the Impact of a Flat Plate on a Water Surface

In naval hydrodynamics most the reseach on the impact of the hull of a vesel to the water surface has focused primarily on mapping the forces on the hull and much less to the formation of the spray. The latter is the topic of the present work, where the spray generated by the impact of a flat plate on a quiescent water surface is studied by experiments and simulations at different impact Froude numbers. Overall two types of sprays are formed: Type I, which is a cloud of droplets and ligaments generated at the impact of the plate's leading edge with the water surface, and Type II, which is formed after the trailing edge of the plate enters the local water surface. Detailed analysis of the experimental data for the Type II spray revealed that the spray envelopes and root point trajectories are independent of Froude number close to the trailing edge, while further away reach higher vertical positions for larger Froude numbers. The numerical simulation captures the general behavior of the Type II spray and agrees favorably with the experimental results. A series of computations with a flexible plate is also reported, where it is shown that increased flexibility reduces the height of the spray and suppresses the formation of droplets.
Estimation of EuroQol 5-Dimensions health status utility values in hereditary angioedema

Objective To estimate health status utility (preference) weights for hereditary angioedema (HAE) during an attack and between attacks using data from the Hereditary Angioedema Burden of Illness Study in Europe (HAE-BOIS-Europe) survey. Utility measures quantitatively describe the net impact of a condition on a patient’s life; a score of 0.0 reflects death and 1.0 reflects full health. Study design and methods The HAE-BOIS-Europe was a cross-sectional survey conducted in Spain, Germany, and Denmark to assess the real-world experience of HAE from the patient perspective. Survey items that overlapped conceptually with the EuroQol 5-Dimensions (EQ-5D) domains (pain/discomfort, mobility, self-care, usual activities, and anxiety/depression) were manually crosswalked to the corresponding UK population-based EQ-5D utility weights. EQ-5D utilities were computed for each respondent in the HAE-BOIS-Europe survey for acute attacks and between attacks. Results Overall, a total of 111 HAE-BOIS-Europe participants completed all selected survey items and thus allowed for computation of EQ-5D-based utilities. The mean utilities for an HAE attack and between attacks were 0.44 and 0.72, respectively. Utilities for an acute attack were dependent on the severity of pain of the last attack (0.61 for no pain or mild pain, 0.47 for moderate pain, and 0.08 for severe pain). There were no significant differences across countries. Mean utilities derived from the study approach compare sensibly with other disease states for both acute attacks and between attacks. Conclusion The impacts of HAE translate into substantial health status disutilities associated with acute attacks as well as between attacks, documenting that the detrimental effects of HAE are meaningful from the patient perspective. Results were consistent across countries with regard to pain severity and in comparison to similar disease states. The results can be used to raise awareness of HAE as a serious disease with wide-ranging personal and social impacts.
Spatio-temporal pattern formation in coupled models of plankton dynamics and sh school motion

Horst Malchowa ; ∗, Birgit Radtkea, Malaak Kallachea, Alexander B. Medvinskyb, Dmitry A. Tikhonovb, Sergei V. Petrovskiic aDepartment of Mathematics and Computer Science, Institute of Environmental Systems Research, University of Osnabr uck, Artilleries tr 34, D-49069 Osnabr uck, Germany bInstitute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142292 Russia cShirshov Institute of Oceanology, Russian Academy of Sciences Nakhimovsky Prospect 36, Moscow 117218, Russia
Integrating Dendrochronology, Climate and Satellite Remote Sensing to Better Understand Savanna Landscape Dynamics in the Okavango Delta, Botswana

This research examines the integration and potential uses of linkages between climate dynamics, savanna vegetation and landscape level processes within a highly vulnerable region, both in terms of climate variability and social systems. We explore the combined applications of two time-series methodologies: (1) climate signals detected in tree ring growth, from published literature, chronologies from the International Tree-Ring Data Bank, and minimal preliminary field data; and (2) new primary production (NPP) data of vegetation cover over time derived from remotely sensed analyses. Both time-series are related to the regional patterns of precipitation, the principle driver of plant growth in the area. The approach is temporally and spatially multiscalar and examines the relationships between vegetation cover, type and amount, and precipitation shifts. We review literature linking dendrochronology, climate, and remotely sensed imagery, and, in addition, provide unique preliminary analyses from a dry study site located on the outer limit of the Okavango Delta. The work demonstrates integration across the different data sources, to provide a more holistic view of landscape level processes occurring in the last 30-50 years. These results corroborate the water-limited nature of the region and the dominance of precipitation in controlling vegetation growth. We present this integrative analysis of vegetation and climate change, as a prospective approach to facilitate the development of long-term climate/vegetation change records across multiple scales.
Genomewide Pattern of Synonymous Nucleotide Substitution in Two Complete Genomes of Mycobacterium tuberculosis

Comparison of the pattern of synonymous nucleotide substitution between two complete genomes of Mycobacterium tuberculosis at 3,298 putatively orthologous loci showed a mean percent difference per synonymous site of 0.000328 ± 0.000022. Although 80.5% of loci showed no synonymous or nonsynonymous nucleotide differences, the level of polymorphism observed at other loci was greater than suggested by previous studies of a small number of loci. This level of nucleotide difference leads to the conservative estimate that the common ancestor of these two genotypes occurred approximately 35,000 ago, which is twice as high as some recent estimates of the time of origin of this species. Our results suggest that a large number of loci should be examined for an accurate assessment of the level of nucleotide diversity in natural populations of pathogenic microorganisms.