Miracle-dz/UniFAR-FTUs huggingface dataset:
Surprisingly High Specificity of the PPD Skin Test for M. tuberculosis Infection from Recent Exposure in The Gambia

Background Options for intervention against Mycobacterium tuberculosis infection are limited by the diagnostic tools available. The Purified Protein Derivative (PPD) skin test is thought to be non-specific, especially in tropical settings. We compared the PPD skin test with an ELISPOT test in The Gambia. Methodology/Principal Findings Household contacts over six months of age of sputum smear positive TB cases and community controls were recruited. They underwent a PPD skin test and an ELISPOT test for the T cell response to PPD and ESAT-6/CFP10 antigens. Responsiveness to M. tuberculosis exposure was analysed according to sleeping proximity to an index case using logistic regression. 615 household contacts and 105 community controls were recruited. All three tests assessed increased significantly in positivity with increasing M. tuberculosis exposure, the PPD skin test most dramatically (OR 15.7; 95% CI 6.6–35.3). While the PPD skin test positivity continued to trend downwards in the community with increasing distance from a known case (61.9% to 14.3%), the PPD and ESAT-6/CFP-10 ELISPOT positivity did not. The PPD skin test was more in agreement with ESAT-6/CFP-10 ELISPOT (75%, p = 0.01) than the PPD ELISPOT (53%, p<0.0001). With increasing M. tuberculosis exposure, the proportion of ESAT-6/CFP-10 positive contacts who were PPD skin test positive increased (p<0.0001), and the proportion of ESAT-6/CFP-10 negative contacts that were PPD skin test negative decreased (p<0.0001); the converse did not occur. Conclusions/Significance The PPD skin test has surprisingly high specificity for M. tuberculosis infection from recent exposure in The Gambia. In this setting, anti-tuberculous prophylaxis in PPD skin test positive individuals should be revisited.
Use of photogrammetry and biomechanical gait analysis to identify individuals

Photogrammetry and recognition of gait patterns are valuable tools to help identify perpetrators based on surveillance recordings. We have found that stature but only few other measures have a satisfying reproducibility for use in forensics. Several gait variables with high recognition rates were found. Especially the variables located in the frontal plane are interesting due to large inter-individual differences in time course patterns. The variables with high recognition rates seem preferable for use in forensic gait analysis and as input variables to waveform analysis techniques such as principal component analysis resulting in marginal scores, which are difficult to interpret individually. Finally, a new gait model is presented based on functional principal component analysis with potentials for detecting individual gait patterns where time course patterns can be marginally interpreted directly in terms of the input variables. In this presentation, the above methods will be discussed exemplified with forensic cases.
An evaluation of invasive fungal sinusitis outcomes with subsite analysis and use of frozen section analysis

Invasive fungal sinusitis (IFS) is an aggressive mycosis of the nasal cavity with frequent extension to adjacent structures. Occurring more commonly in immunocompromised individuals, prognosis is typically poor despite aggressive treatment. This study aims to examine postoperative outcomes and survival of a cohort of fungal sinusitis patients at an academic center, as well as identify causes of death in IFS patients.
Body composition and tissue distribution from birth to 14 months for three biological types of beef heifers.

Thirty-four heifers were sampled randomly from each of the Hereford (He), Charolais (Ch) and Simmental (Si) herds at the U.S. Meat Animal Research Center at 2 d to 14 mo of age to examine body chemical composition and tissue distribution. Six heifers per breed were slaughtered after calorimetry at 2 d, 3 mo, 7 mo, 10 mo and 14 mo of age, and four others at 8 mo, to measure weight of empty body (EBW), water, fat, ash and protein as residual, in four fractions: carcass (CAR), head, hide and shanks (HHS), gastrointestinal tract plus internal fat (GIF) and visceral organs plus blood (VOB). Fasted live weight from birth to 14 mo increased from 39 to 414 kg for Ch, 38 to 385 kg for Si and 33 to 356 kg for He. Corresponding mean composition of EBW increased from 58 to 67% CAR and from 7 to 13% GIF but declined from 26 to 15% HHS and from 9 to 6% VOB. The water content of EBW declined from 73 to 51%, protein from 20 to 18% and ash from 4.3 to 3.5%, whereas fat increased from 3 to 28% and protein content of fat-free OM increased from 22% to 26%. Composition of CAR was similar to EBW but fat content increased more with age in GIF, less in HHS and least in VOB. Distribution of fat-free tissue changed from 58 to 66% in CAR, 26 to 18% in HHS, 7 to 8% in GIF and 9 to 8% in VOB. The EBW of Ch contained more CAR but less HHS than EBW of Si and HE. The EBW of Si and Ch contained more water and protein and less FAT than EBW of HE. The fatter He had proportionately less of their fat-free tissue in CAR (63%) and more in HHS (21%) and GIF (9%) than the Ch (66, 19, and 8%), with Si (64, 20 and 8%) intermediate. These age and breed differences in composition and tissue distribution may explain some of the variation in maintenance requirements.
Enhancing Path Stability Towards the Provision of Multimedia Support in Vehicular Ad Hoc Networks

The recent advances and wide availability of wireless access technologies and inter-vehicle communication systems are expected to culminate in the integration of different wireless networks such as the IEEE 802.11, 3G/4G, and WiMax, multimedia and sensor networks in the next generation vehicular networks. However, due to high mobility of vehicles, several issues remain to be resolved before real-time multimedia based applications over VANETs become a reality. In this paper, we propose to study the provision of multimedia support in VANET, and present an efficient Path Stability Protocol, which we refer to as PASTA, as an additional module to MAC layer protocols that aims at preventing path breaks between vehicles that are frequently within reach of each other but not necessarily on a continuous basis. We discuss the implementation of our protocol, and report on its performance evaluation using a wide range of realistic scenarios. Our results indicate that our PASTA protocol decreases significantly the end-to-end latency as well as the network jitter.
Preparing primary school teachers to teach religious education

Under the guidelines for Initial Teacher Training, all potential primary teachers are required to learn about teaching religious education. However, religious education is not a high priority on ITT programmes and trainees may often have little introduction to it. Given the sensitive nature of religious education, what is the best way to prepare trainees for teaching religious education, and how far do we need to take into account their views about the subject? This article reports on a study involving trainees on a one‐year PGCE course. All the students were preparing to teach in primary schools and were not specialist religious education trainees. The aim of the study was to discover how trainees felt about teaching religious education in the primary school and how far their feelings linked to their views about religion. The conclusions suggest that any effective preparation of the trainees needs to recognise the diversity of their starting points and allow them opportunity to reflect on their views of religion and religious education.
Protective Roles of Natural IgM Antibodies

Antibodies are a vital part of the armamentarium of the adaptive immune system for the fine-tuning of the recognition and response to foreign threats. However, in health there are some types of antibodies that instead recognize self-antigens and these contribute to the enhancement of primitive innate functions. This repertoire of natural IgM antibodies is postulated to have been selected during immune evolution for their contributions to critical immunoregulatory and housekeeping properties. The clearance of dying cells is one of the most essential responsibilities of the immune system, which is required to prevent uncontrolled inflammation and autoimmunity. In the murine immune system, natural IgM antibodies that recognize apoptotic cells have been shown to enhance the phagocytic clearance of dead and dying cells and to suppress innate immune signaling pathways. In the mouse, natural IgM are often the products of B-1 cell clones that arise during immune development without an absolute requirement for exogenous antigenic stimulation. In patients with systemic lupus erythematosus, IgM autoantibodies, which bind to neo-epitopes on apoptotic cells, have been demonstrated to be present at significantly higher levels in patients with lower disease activity and with less severe organ damage. While certain specificities of IgM autoantibodies correlate with protection from lupus renal disease, others may convey protective properties from lupus-associated atherosclerotic cardiovascular disease. New and unexpected insights into the functional roles of IgM antibodies are still emerging, especially regarding the functions of natural antibodies. Herein, we review recent progress in our understanding of the potential roles of natural IgM autoantibodies in the regulation of immune homeostasis and for protection from autoimmune and inflammatory diseases.
A Reinterpretation of Historic Aquifer Tests of Two Hydraulically Fractured Wells by Application of Inverse Analysis, Derivative Analysis, and Diagnostic Plots

Aquifer test methods have greatly improved in recent years with the advent of inverse analysis, derivative analysis, and diagnostic plots. Updated analyses of past aquifer tests allow for improved interpretations of the data to enhance the knowledge and the predictive capabilities of the flow system. This work thoroughly reanalyzes a series of pre- and post-hydraulic fracturing, single-well aquifer tests conducted in two crystalline rock wells in New Hampshire as part of an early 1970’s study. Previous analyses of the data had relied on older manual type-curve methods for predicting the possible effects of hydraulic fracturing. This work applies inverse analysis, derivative analysis, and diagnostic plots to reanalyze the 1970’s aquifer test data. Our results demonstrate that the aquifer tests were affected by changes in flow regimes, dewatering of the aquifer and discrete fractures, and changes due to well development. Increases in transmissivities are related to well development prior to hydraulic fracturing, propagation of a single, vertical fracture hydraulically connecting the two wells after stimulation and expansion of troughs of depression. After hydraulic fracturing, the estimated total yield of the individual wells increased by 2.5 times due to the hydraulic fracturing. However, the wells may be receiving water from the same source, and well interference may affect any significant increase in their combined yield. Our analyses demonstrate the value in applying inverse analysis, derivative analysis, and diagnostic plots over the conventional method of manual type-curve analysis. In addition, our improvement in the aquifer test interpretation of the 1970’s test data has implications for more reliable estimates of sustained well yields.
The Estimation of Reliability in Longitudinal Models

Despite the increasing attention devoted to the study and analysis of longitudinal data, relatively little consideration has been directed toward understanding the issues of reliability and measurement error. Perhaps one reason for this neglect has been that traditional methods of estimation (e.g. generalisability theory) require assumptions that are often not tenable in longitudinal designs. This paper first examines applications of generalisability theory to the estimation of m easurement error and reliability in longitudinal research, and notes how factors such as missing data, correlated errors, and true score instability prohibit traditional variance com ponent estimation. Next, we discuss how estimation methods using restricted maximum likelihood can account for these factors, thereby providing m any advantages over traditional estimation methods. Finally, we provide a substantive exam ple illustrating these advantages, and include brief discussions of programming and software considerations.
Systematic review of ethnic variation in the phenotype of Behcet's disease

Objective: To systematically review the strength of evidence that supports the premise that there are different expressions in the clinical phenotype of Behcet's disease (BD) in different ethnic groups. Methods: The hierarchy of evidence and inclusion criteria were decided prior to the search for relevant literature. We searched Medline and Embase databases between 1966 and March 2005 for publications related to epidemiology of Behcet's disease or syndrome. Relevant papers were extracted in hard copy and the references of all these papers were then hand searched for further articles. Results: Four population‐based studies, of which two were from Turkey, and seven non‐population‐based comparative studies were found. The majority of literature identified were case series and were not included in the review. There were insufficient cross‐sectional studies from different populations to be able to compare phenotypic differences. None of the comparative studies found evidence of a difference in the clinical expression of BD between ethnic groups. Conclusions: There is insufficient evidence to support the premise that there are different expressions in the clinical phenotype of BD in different ethnic groups. Population‐based, cross‐sectional surveys or case–control studies using standardized criteria and clear ethnic definitions are suggested to investigate this hypothesis further.
Endoplasmic reticulum localization of Sec12p is achieved by two mechanisms: Rer1p-dependent retrieval that requires the transmembrane domain and Rer1p-independent retention that involves the cytoplasmic domain

Yeast Sec12p is a type II transmembrane protein in the ER, which is essential for the formation of transport vesicles. From biochemical and morphological lines of evidence, we have proposed that Sec12p is localized to the ER by two mechanisms: static retention in the ER and dynamic retrieval from the early Golgi compartment. We have also shown that Rer1p, a membrane protein in the Golgi, is required for correct localization of Sec12p. In the present study, we have performed a systematic analysis to determine the ER localization signals in Sec12p corresponding to these two mechanisms. Both the transmembrane domain (TMD) and the NH2-terminal cytoplasmic domain of Sec12p show the ability to localize the protein to the ER. The effect of the TMD is potent and sufficient by itself for the ER localization and is strongly dependent on Rer1p. On the other hand, the cytoplasmic domain shows a moderate ER-localization capability which is independent of Rer1p. The rate of mannosyl modification has been measured to distinguish between retention and retrieval. The cytoplasmic domain significantly delays the transport from the ER to the cis-Golgi. In contrast, the TMD shows only a subtle retardation in the transport from the ER to the cis-Golgi but strictly prevents the transport beyond there. From these observations, we conclude that the TMD mainly acts as the retrieval signal and the cytoplasmic domain contains the retention signal. This study not only supports the two-mechanisms hypothesis but also provides powerful tools to dissect the two.
High-dimensional mapping of the hippocampus in depression.

OBJECTIVE Abnormalities of the hippocampus may play a role in the pathophysiology of depression, but efforts to identify a structural abnormality in this brain structure among depressed patients have produced mixed results. Previous research may have been limited by exclusive reliance on measures of hippocampal volume. High-dimensional brain mapping is a new analytic method that quantitatively characterizes the shape as well as volume of a brain structure. In this study, high-dimensional brain mapping was used to evaluate hippocampal shape and volume in patients with major depressive disorder and healthy comparison subjects. METHOD By using magnetic resonance imaging, brain scans were obtained from 27 patients with major depressive disorder and 42 healthy comparison subjects. High-dimensional brain mapping generated a series of 10 variables (components) that represented hippocampal shape, and hippocampal volumes were also computed. Analysis of variance techniques were used to compare depressed patients and comparison subjects on hippocampal shape and volume. RESULTS While the depressed patients and comparison subjects did not differ in hippocampal volume, there were highly significant group differences in hippocampal shape. The two groups did not overlap on a discriminant function computed from a model comprising the 10 components. The pattern of hippocampal surface deformation in the depressed patients suggested specific involvement of the subiculum. CONCLUSIONS Patients with major depression may have structural abnormalities of the hippocampus that can be detected by analysis of hippocampal shape but not volume. A specific defect in the subiculum could have widespread effects throughout neurocircuits that appear to be abnormal in depression.
Familial loading for alcoholism and offspring behavior: mediating and moderating influences.

BACKGROUND Familial loading for alcoholism is an important marker of risk for early-onset alcohol problems, but the early expression of this risk in community samples of children is understudied. METHODS This study tested, for 452 8- and 10-year-old children, whether the density of alcohol problems in their biological relatives was associated with externalizing behaviors that are risk factors for later alcohol problems. RESULTS Density of alcohol problems in first- and second-degree biological relatives was associated with behavioral disinhibition (BD; e.g., poor inhibitory control, attentional shifting, β = 0.10, p = 0.04) and conduct problems (CP; i.e., defiance, aggression, delinquency, β = 0.18, p = 0.00). These relations were moderated by parenting practices (parental warmth, discipline consistency, and parental monitoring). The density-behavior association lost statistical significance when at least 2 of 3 parenting practices were rated above median levels for the sample (p = 0.67 to 0.36). The density-behavior association was mediated by current demographic advantage (p = 0.00 for BD, p = 0.00 for CP), current maternal mental health (p = 0.01 for BD, p = 0.00 for CP), and current maternal deviant behavior (for CP only, p = 0.01). CONCLUSIONS Findings support previously proposed but untested pathways in etiologic models of alcoholism and show the potentially important role of active parenting in reducing the expression of inherited vulnerability to alcoholism in childhood.
HST/STIS spectroscopy of the environment in the starburst core of M82

We present high-resolution optical HST Space Telescope Imaging Spectrograph (STIS) observations made with two slits crossing four of the optically brightest starburst clumps in the vicinity of the nucleus of M82. These provide Hα kinematics, extinction, electron density and emission measures. From the radial velocity curves derived from both slits we confirm the presence of a stellar bar. We also find that the super star cluster M82-A1 has a position and radial velocity consistent with it being at the end of one of the unique x2 bar orbits formed by an inner Lindblad resonance. We derive a new model for the orientation of the bar and disc with respect to the main starburst clumps, and propose that clump A has formed within the bar region as a result of gas interactions between the bar orbits, whereas region C lies at the edge of the bar and regions D and E are located further out from the nucleus but heavily obscured. We derive extremely high interstellar densities of 500–900 cm, corresponding to ISM pressures of P/k ≈ 0.5–1.0 × 10 cm K, and discuss the implications of the measured gas properties surrounding the nuclear star clusters on the production and evolution of the galactic wind. Despite varying pressures, the ionization parameter is uniform down to parsec-scales, and we discuss why this might be so. Where the signal-to-noise (S/N) of our spectra are high enough, we identify multiple emission-line components. Through detailed Gaussian line-fitting, we identify a ubiquitous broad (200–300 km s) underlying component to the bright Hα line, and discuss the physical mechanism(s) that could be responsible for such widths. We conclude that the evaporation and/or ablation of material from interstellar gas clouds caused by the impact of the high-energy photons and fast-flowing cluster winds produces a highly turbulent layer on the surface of the clouds from which the emission arises. Subject headings: galaxies: individual(M82) – galaxies: ISM – galaxies: starburst – galaxies: star clusters – galaxies: kinematics and dynamics – ISM: evolution
Mechanical and energetic scaling relationships of running gait through ontogeny in the ostrich (Struthio camelus)

SUMMARY It is unclear whether small animals, with their high stride frequency and crouched posture, or large animals, with more tendinous limbs, are more reliant on storage and return of elastic energy during locomotion. The ostrich has a limb structure that appears to be adapted for high-speed running with long tendons and short muscle fibres. Here we investigate biomechanics of ostrich gait through growth and, with consideration of anatomical data, identify scaling relationships with increasing body size, relating to forces acting on the musculoskeletal structures, effective mechanical advantage (EMA) and mechanical work. Kinematic and kinetic data were collected through growth from running ostriches. Joint moments scaled in a similar way to the pelvic limb segments as a result of consistent posture through growth, such that EMA was independent of body mass. Because no postural change was observed, relative loads applied to musculoskeletal tissues would be predicted to increase during growth, with greater muscle, and hence tendon, load allowing increased potential for elastic energy storage with increasing size. Mass-specific mechanical work per unit distance was independent of body mass, resulting in a small but significant increase in the contribution of elastic energy storage to locomotor economy in larger ostriches.
The in vitro methylation of DNA by a minor groove binding methyl sulfonate ester.

The preparation of sequence and groove specific DNA methylating agents based on N-methylpyrrolecarboxamide subunits appended with an O-methyl sulfonate ester functionality (MeOSO2(CH2)2-Lex) has previously been described [Zhang, Y. , Chen, F. -X. , Mehta, P., and Gold, B. (1993) Biochemistry 32,7954-7965]. In contrast to simple methyl sulfonate esters, e.g., methyl methanesulfonate (MMS), which predominantly methylate at 7-guanine, MeOSO2-(CH2)2-Lex affords N3-methyladenine (3-MeAde) as its major adduct. Using competitive ELISA determinations, the methylation at major and minor groove sites in calf thymus DNA by MeOSO2(CH2)2-Lex has been precisely quantitated. The yields of N7-methylguanine (7-MeGua), 3-MeAde, and O6-methyldeoxyguanosine (6-Me-dGuo) are 0.424, 3.195, and 0.0027 mmol of adduct/mol of DNA, respectively, using 10 microM MeOSO2(CH2)2-Lex and 100 microM DNA. This compares to 0.773, 0.072, and 0.0033 mmol of adduct/mol of DNA for 7-MeGua, 3-MeAde, and 6-Me-dGuo, respectively, using MMS. The increase in the yield of 3-MeAde due to the minor groove equilibrium binding properties of MeOSO2(CH2)2-Lex is approximately 40-fold relative to MMS.