Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effects of HIV on the Sensitivity of a Whole Blood IFN-γ Release Assay in Zambian Adults with Active Tuberculosis

Background Interferon gamma release assays (IGRA) are replacing the tuberculin skin test (TST) as a diagnostic tool for Mycobacterium tuberculosis infection. However research into the test's performance in the high HIV-TB burden setting is scarce. This study aimed to define the sensitivity of an IGRA, QuantiFERON-TB® Gold In-Tube (QGIT), in adult Zambian patients with active smear-positive tuberculosis. Secondary outcomes focussed on the effect of HIV on the test's performance. Principal Findings Patients attending government health clinics were recruited within 1 month of starting treatment for TB. Subjects were tested with QGIT and TST. T lymphocyte counts were estimated (CD3+, CD4+, CD8+). QGIT was performed for 112 subjects. 83/112 were QGIT positive giving an overall sensitivity of 74% [95%CI: 66,82]. A marked decrease in sensitivity was observed in HIV positive patients with 37/59 (63%) being QGIT positive compared to 31/37 (84%) HIV negative patients [chi2 p = 0.033]. Low CD4+ count was associated with increases in both indeterminate and false-negative results. Low CD4+ count in combination with high/normal CD8+ count was associated with false-negative results. TST was recorded for 92 patients, 62/92 were positive, giving a sensitivity of 67% [95%CI: 58,77]. Although there was little difference in the overall sensitivities, agreement between TST and QGIT was poor. Conclusions QGIT was technically feasible with results in HIV negative subjects comparable to those achieved elsewhere. However, where under-treated HIV is prevalent, an increased proportion of both indeterminate and false-negative QGIT results can be expected in patients with active TB. The implications of this for the diagnosis of LTBI by QGIT is unclear. The diagnostic and prognostic relevance of IGRAs in high burden settings needs to be better characterised.
Prognosis in severe chronic obstructive pulmonary disease.

The prognosis of 187 patients with severe chronic obstructive pulmonary disease has been evaluated by use of the life table method. All patients had a FEV1 less than 60% of VC and below 1.5 1. The observation time ranged from 4 years and 4 months to 7 years and 4 months. The cumulative survival rate in the whole material was 71 % after 3 years and 47% after 6 ýears, results which are very close to the survival found by other authors. Calculations are presented of the survival of FEV1 subgroups and of clinical functional groups separately and combined. These two classifications have a good correlation to survival, and it is demonstrated that the combination of functional group and FEV1 subgroups adds more information regarding the prognosis than that obtained through FEV1 alone. Among patients with earlier pulmonary tuberculosis the prognosis was related only to the degree of pulmonary obstruction. The expected increase in lethality with advancing age was demonstrated, but the mortality was relatively higher in the younger age group when compared to the general population of the same age. The prognosis of patients with cor pulmonale was considerably worse than of patients without cor pulmonale, even when the higher degree of severe airway obstruction was considered.
Perceptual Reinforcement of Speech Signal Based on Partial Specific Loudness

In the presence of background noise, the perceptual loudness of speech signal significantly decreases, resulting in the deterioration of intelligibility and clarity. In this letter, we propose a novel approach to enhance the perceived quality of the speech signal when the additive noise cannot be directly controlled. Instead of controlling the background noise, we propose to reinforce the speech signal so that it can be heard more clearly in noisy environments. To find a suitable reinforcement rule, the loudness perception model proposed by Moore et al. is adopted. Experimental results show that the loudness of the reinforced signal can be maintained at the level almost the same as that of the original noise-free speech, and the proposed algorithm can enhance the perceived speech quality under various noise environments.
Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation

There is an ongoing discussion in the literature on whether human mitochondrial DNA (mtDNA) evolves neutrally. There have been previous claims for natural selection on human mtDNA based on an excess of non-synonymous mutations and higher evolutionary persistence of specific mitochondrial mutations in Arctic populations. However, these findings were not supported by the reanalysis of larger datasets. Using a geographical framework, we perform the first direct test of the relative extent to which climate and past demography have shaped the current spatial distribution of mtDNA sequences worldwide. We show that populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature. These associations were unique to mtDNA; we could not find a similar pattern in any other genetic marker. We were able to identify two correlated non-synonymous point mutations in the ND3 and ATP6 genes characterized by a clear association with temperature, which appear to be plausible targets of natural selection producing the association with climate. The same mutations have been previously shown to be associated with variation in mitochondrial pH and calcium dynamics. Our results indicate that natural selection mediated by climate has contributed to shape the current distribution of mtDNA sequences in humans.
Biphasic changes in left ventricular function during hyperdynamic endotoxemia.

Cardiac contractility was studied in a clinically relevant conscious swine model simulating human hemodynamics during endotoxemia. The slope of the end-systolic pressure-volume relationship [end-systolic elastance ( E ES)] was used as a load-independent contractility index. Chronic instrumentation in 10 pigs included two pairs of endocardial ultrasonic crystals for measuring internal major and minor axial dimensions of the left ventricle, a micromanometer for left ventricular pressure measurement, and a thermodilution pulmonary artery catheter. After a 10-day recovery period, control measurements of cardiac hemodynamic function were obtained. The following week, Escherichia coli endotoxin (10 μg ⋅ kg-1 ⋅ h-1) was administered intravenously for 24 h. E ES increased 1 h after endotoxin infusion and decreased beyond 7 h. The later hemodynamic changes resembled human cardiovascular performance during endotoxemia more closely than the changes during the acute phase. E ES decreased in the later phase. A similar biphasic response of E ES has been reported during a tumor necrosis factor-α (TNF) challenge. Even though plasma TNF was highest at 1 h and declined thereafter in this study, no consistent relationship between TNF and E ES was identified, and TNF levels did not correlate directly with the changes in E ES.
DREAMS OF SUBJECTS WITH BILATERAL HIPPOCAMPAL LESIONS

INTRODUCTION Experimental evidence has been recently accumulated suggesting that dreams represent a partial perception of the visual concomitants of a potentially continuously ongoing process of encoding longterm memories (Torda ( 1967 a, b, 1968 a, b, c, 1969 a, b) ). Dreams appear to be memory traces of old and new events woven into ever changing stories under emotional impact. The manifest content of dreams is heavily loaded with percepts originating in recent daily experiences (Greenberg & Leidcrman ( 1966) ). In order to gain a better understanding of the nature of dreams, it occurred, therefore, to study the dreams of subjects with amnesia for recent events.
The bio-corona and its impact on nanomaterial toxicity

Abstract The rapidly growing application of nano-sized materials and nano-scaled processes will result in increased exposure of humans and the environment. The small size of nanomaterials (NM) comparable with molecular building blocks of cells raises concerns that their toxic potential cannot be extrapolated from studies of larger particles due to their unique physico-chemical properties. These properties are also responsible that NM rapidly adsorb various (bio)molecules when introduced into complex physiological or natural environments. As the thus formed protein/biomolecule ‘corona’ seems to affect the NM’ in situ identity, an understanding of its toxicological relevance and the biophysical forces regulating corona formation is needed but not yet achieved. This review introduces our current concept of corona formation and evolution and present analytical methods for corona profiling. We discuss toxicity mechanisms potentially affected by the biomolecule corona, including NM cellular uptake and impact on components of the blood system. Further, we comment on pending knowledge gaps and challenges, which need to be resolved by the field. We conclude by presenting a tiered systems biology-driven approach recommended to mechanistically understand the coronas’ nanotoxicological relevance and predictive potential.
Cellulose- and Xylan-Degrading Thermophilic Anaerobic Bacteria from Biocompost

ABSTRACT Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a Clostridium clariflavum strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.
Evaluation of power prediction equations: peak vertical jumping power in women.

PURPOSE The purpose of this investigation was to: 1) compare actual peak power (PPactual) to estimated values (PPest) derived from three different prediction equations (Sayers and Harman), 2) determine the ability of the prediction formulas to monitor change following 6 wk of plyometric training, and 3) generate a new regression model. METHODS colon; Twenty college females (age = 20.1 +/- 1.6 yr; body mass = 65.9 +/- 8.9 kg) were randomly assigned to a control or intervention group. Pre- and posttest countermovement jump (CMJ) height and PPactual were determined simultaneously on a force platform. Body mass and maximal CMJ height were used to predict peak power. RESULTS colon; All three PPest were significantly correlated 0.84-0.99) and post (r = 372.4 W) was significantly less to PPactual and to each other on pre (r = 0.88-0.99) tests. PPactual (2425.4 +/- 2920.8 +/- 482.6 W; CMJ = 2925.1 +/- 409.7 than PPest (Sayers: SJ = 473.0 W) but was not different from PPest (Harman: 2585.0 +/- 409.7 W). Posttests revealed similar differences between PPactual and PPest for the intervention group, however no significant differences were observed for the control group. Mean differences from pre and posttests did not differ within or between PPest. Regression analysis determined the formula: ppest = 65.1 x (jump height) + 25.8 x (body mass) - 1413.1 (R = 0.92; SEE = 120.8), which slightly determined (0.77%) peak power is compared with PPactual in our cross-validation sample (n = 7) CONCLUSIONS colon; Changes in peak power is accurate using any of the regression equations; however, the new prediction formula and that of Harman seem to more precisely estimate peak power. Strict jumping technique along with simultaneous measurement of power and jump height should be used as the standard for comparison.
Transglutaminase Activity, Protein, and mRNA Expression Are Increased in Progressive Supranuclear Palsy

Transglutaminases catalyze the covalent cross-linking of substrate proteins to form insoluble protein complexes that are resistant to degradation. Our previous studies demonstrated that transglutaminase-induced cross-linking of tau proteins occurs in Alzheimer disease and progressive supranuclear palsy (PSP). The current study was designed to measure transglutaminase enzyme activity and the mRNA and protein levels of 3 transglutaminase isoforms that are expressed in human brain. Overall, transglutaminase activity was significantly increased in the globus pallidus (182% of control) and pons in PSP (171% of control) but not the occipital cortex (a region spared from pathology). Using a Spearman rank correlation test, we found that tissues with more transglutaminase-activity had more neurofibrillary tangles. Protein and mRNA levels of transglutaminase 1 were increased in globus pallidus of PSP as compared to controls. There were also significantly higher mRNA levels of the short form of transglutaminase 2 in globus pallidus of PSP (974% of control). Transglutaminase 1 mRNA and the long isoform of transglutaminase 2 mRNA (2212% of control) were significantly higher in PSP in the dentate of cerebellum. Together, these findings suggest that transglutaminase 1 and 2 enzymes may be involved in the formation and/or stabilization of neurofibrillary tangles in selectively vulnerable brain regions in PSP. These transglutaminases may be potential targets for therapeutic intervention.
On genomic repeats and reproducibility

RESULTS Here, we present a comprehensive analysis on the reproducibility of computational characterization of genomic variants using high throughput sequencing data. We reanalyzed the same datasets twice, using the same tools with the same parameters, where we only altered the order of reads in the input (i.e. FASTQ file). Reshuffling caused the reads from repetitive regions being mapped to different locations in the second alignment, and we observed similar results when we only applied a scatter/gather approach for read mapping-without prior shuffling. Our results show that, some of the most common variation discovery algorithms do not handle the ambiguous read mappings accurately when random locations are selected. In addition, we also observed that even when the exact same alignment is used, the GATK HaplotypeCaller generates slightly different call sets, which we pinpoint to the variant filtration step. We conclude that, algorithms at each step of genomic variation discovery and characterization need to treat ambiguous mappings in a deterministic fashion to ensure full replication of results. AVAILABILITY AND IMPLEMENTATION Code, scripts and the generated VCF files are available at DOI:10.5281/zenodo.32611. CONTACT calkan@cs.bilkent. edu.tr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
PowerNap: eliminating server idle power

Data center power consumption is growing to unprecedented levels: the EPA estimates U.S. data centers will consume 100 billion kilowatt hours annually by 2011. Much of this energy is wasted in idle systems: in typical deployments, server utilization is below 30%, but idle servers still consume 60% of their peak power draw. Typical idle periods though frequent--last seconds or less, confounding simple energy-conservation approaches. In this paper, we propose PowerNap, an energy-conservation approach where the entire system transitions rapidly between a high-performance active state and a near-zero-power idle state in response to instantaneous load. Rather than requiring fine-grained power-performance states and complex load-proportional operation from each system component, PowerNap instead calls for minimizing idle power and transition time, which are simpler optimization goals. Based on the PowerNap concept, we develop requirements and outline mechanisms to eliminate idle power waste in enterprise blade servers. Because PowerNap operates in low-efficiency regions of current blade center power supplies, we introduce the Redundant Array for Inexpensive Load Sharing (RAILS), a power provisioning approach that provides high conversion efficiency across the entire range of PowerNap's power demands. Using utilization traces collected from enterprise-scale commercial deployments, we demonstrate that, together, PowerNap and RAILS reduce average server power consumption by 74%.
Reduced Content of Homogalacturonan Does Not Alter the Ion-Mediated Increase in Xylem Hydraulic Conductivity in Tobacco

Xylem hydraulic conductivity (Ks) in stems of tobacco (Nicotiana tabacum) wild-type SR1 was compared to that of PG7 and PG16, two transgenic lines with increased levels of expression of the gene encoding the Aspergillus niger endopolygalacturonase (AnPGII). Activity of AnPGII removes in planta blocks of homogalacturonan (HG) with deesterified carboxyls, thus increasing the degree of neutrality of pectins. The effect of K+ was tested in increasing stem Ks using model plants with more neutral polysaccharides in primary walls and, hence, in intervessel pit membranes. Ks measured with deionized water was compared to that with KCl solutions at increasing concentrations (ΔKs, %). Plants transformed for HG degree of neutrality showed a dwarfed phenotype, but ΔKs did not differ among the three experimental groups. The ion-mediated hydraulic effect saturated at a KCl concentration of 25 mm in SR1 plants. All the three tobacco lines showed ΔKs of around +12.5% and +17.0% when perfused with 10 and 25 mm KCl, respectively. Because modification of HG content did not influence ion-mediated hydraulic enhancement, we suggest that pectin components other than HG, like rhamnogalacturonan-I and/or rhamnogalacturonan-II, might play important roles in the hydrogel behavior of pit membranes.
The injured eye

Eye injuries come at a high cost to society and are avoidable. Ocular blast injuries can be primary, from the blast wave itself; secondary, from fragments carried by the blast wind; tertiary; due to structural collapse or being thrown against a fixed object; or quaternary, from burns and indirect injuries. Ballistic eye protection significantly reduces the incidence of eye injuries and should be encouraged from an early stage in Military training. Management of an injured eye requires meticulous history taking, evaluation of vision that measures the acuity and if there is a relative pupillary defect as well as careful inspection of the eyes, under anaesthetic if necessary. A lateral canthotomy with cantholysis should be performed immediately if there is a sight-threatening retrobulbar haemorrhage. Systemic antibiotics should be prescribed if there is a suspected penetrating or perforating injury. A ruptured globe should be protected by an eye shield. Primary repair of ruptured globes should be performed in a timely fashion. Secondary procedures will often be required at a later date to achieve sight preservation. A poor initial visual acuity is not a guarantee of a poor final result. The final result can be predicted after approximately 3–4 weeks. Future research in eye injuries attempts to reduce scarring and neuronal damage as well as to promote photoreceptor rescue, using post-transcriptional inhibition of cell death pathways and vaccination to promote neural recovery. Where the sight has been lost sensory substitution of a picture from a spectacle mounted video camera to the touch receptors of the tongue can be used to achieve appreciation of the outside world.
A progressive random walk algorithm for sampling continuous fitness landscapes

A number of fitness landscape analysis approaches are based on random walks through discrete search spaces. Applying these approaches to real-encoded problems requires the notion of a random walk in continuous space. This paper proposes a progressive random walk algorithm and the use of multiple walks to sample neighbourhood structure in continuous multi-dimensional spaces. It is shown that better coverage of a search space is provided by progressive random walks than simple unbiased random walks.
Increased Noise Levels Have Different Impacts on the Anti-Predator Behaviour of Two Sympatric Fish Species

Animals must avoid predation to survive and reproduce, and there is increasing evidence that man-made (anthropogenic) factors can influence predator−prey relationships. Anthropogenic noise has been shown to have a variety of effects on many species, but work investigating the impact on anti-predator behaviour is rare. In this laboratory study, we examined how additional noise (playback of field recordings of a ship passing through a harbour), compared with control conditions (playback of recordings from the same harbours without ship noise), affected responses to a visual predatory stimulus. We compared the anti-predator behaviour of two sympatric fish species, the three-spined stickleback (Gasterosteus aculeatus) and the European minnow (Phoxinus phoxinus), which share similar feeding and predator ecologies, but differ in their body armour. Effects of additional-noise playbacks differed between species: sticklebacks responded significantly more quickly to the visual predatory stimulus during additional-noise playbacks than during control conditions, while minnows exhibited no significant change in their response latency. Our results suggest that elevated noise levels have the potential to affect anti-predator behaviour of different species in different ways. Future field-based experiments are needed to confirm whether this effect and the interspecific difference exist in relation to real-world noise sources, and to determine survival and population consequences.
Physical Properties and Test Methods for Expanded Polytetrafluoroethylene (PTFE) Grafts

This paper will assist the Food and Drug Administration's efforts to develop rational standards for vascular grafts. Since very little technical information has been published on the physical properties of polytetrafluoroethylene (PTFE) grafts, this paper will also address the concerns of ASTM, clinicians, and graft manufacturers. Detailed descriptions are given for current test methods designed to measure physical dimensions, bulk density, porosity, water entry pressure, longitudinal tensile strength, radial tensile strength, suture retention strength, burst strength, and percent sintered. Grafts made by all three current suppliers were tested according to the described test methods. The results indicate that currently available PTFE grafts have very similar inner surfaces with widely varying outer surfaces. Though variations in design directly influence physical strength, all currently available PTFE grafts appear to possess adequate physical properties to ensure safe clinical use.