Miracle-dz/UniFAR-FTUs huggingface dataset:
Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus

Exposure to Staphylococcus aureus has a variety of outcomes, from asymptomatic colonization to fatal infection. Strong evidence suggests that host genetics play an important role in susceptibility, but the specific host genetic factors involved are not known. The availability of genome-wide single nucleotide polymorphism (SNP) data for inbred Mus musculus strains means that haplotype association mapping can be used to identify candidate susceptibility genes. We applied haplotype association mapping to Perlegen SNP data and kidney bacterial counts from Staphylococcus aureus-infected mice from 13 inbred strains and detected an associated block on chromosome 7. Strong experimental evidence supports the result: a separate study demonstrated the presence of a susceptibility locus on chromosome 7 using consomic mice. The associated block contains no genes, but lies within the gene cluster of the 26-member extended kallikrein gene family, whose members have well-recognized roles in the generation of antimicrobial peptides and the regulation of inflammation. Efficient mixed-model association (EMMA) testing of all SNPs with two alleles and located within the gene cluster boundaries finds two significant associations: one of the three polymorphisms defining the associated block and one in the gene closest to the block, Klk1b11. In addition, we find that 7 of the 26 kallikrein genes are differentially expressed between susceptible and resistant mice, including the Klk1b11 gene. These genes represent a promising set of candidate genes influencing susceptibility to Staphylococcus aureus.
Relationship between Isokinetic Strengths, Subjective Knee Scores, and Functional Performance after ACL Reconstruction

The purpose of this study is to examine the relationship between isokinetic strengths, subjective knee scores, and functional performance in patients with an ACL-reconstructed knee. [Methods] Fifty-five male patients between the ages of 16~53 years were enrolled in this study. At the time of testing, a mean 19.7 months had elapsed since the patients had received ACL reconstruction. Muscle strength of the affected knee was measured using an isokinetic dynamometer at the following velocities; 60, 180, 240°/s. The patients scored their affected knee function using 3 subjective knee scores: Lysholm, IKDC, and the Tegner Scores. Functional performance of the affected knee was measured using the one leg hop test for distance. [Results] Isokinetic measurements showed a significant correlation only with the Tegner score. At 60°/s, peak torque (r=.322, p<.05) and peak torque to weight ratio, also written as peak torque % body weight (r=.395, p<.01), were positively correlated with the Tegner score. At 180°/s, peak torque % body weight (r=.336, p<.05), total work (r=.354, p<.05), and total work % body weight (r=.400, p<.01) were positively correlated with the Tegner score. At 240°/s, peak torque % body weight (r=.304, p<.05), total work (r=.318, p<.05), and total work % body weight (r=.331, p<.05) were positively correlated. At 60°/s, all isokinetic measurements for both extensors and flexors were significantly correlated with the functional performance of that knee (p<.01), of which the total work % body weight showed the strongest correlation (r=.600, p<.001). At 180°/s, all isokinetic measurements, except for total work by flexor muscles, were significantly correlated with functional performance (p<.05). At 240°/s, all isokinetic measurements were significantly correlated with functional performance (p<.05). [Conclusion] The clinical information derived from measuring total work, as a reflection of knee function, has been undervalued and is as good as that derived from peak torque.
The neurology of syntax: Language use without Broca's area

A new view of the functional role of the left anterior cortex in language use is proposed. The experimental record indicates that most human linguistic abilities are not localized in this region. In particular, most of syntax (long thought to be there) is not located in Broca's area and its vicinity (operculum, insula, and subjacent white matter). This cerebral region, implicated in Broca's aphasia, does have a role in syntactic processing, but a highly specific one: It is the neural home to receptive mechanisms involved in the computation of the relation between transformationally moved phrasal constituents and their extraction sites (in line with the Trace-Deletion Hypothesis). It is also involved in the construction of higher parts of the syntactic tree in speech production. By contrast, basic combinatorial capacities necessary for language processing – for example, structure-building operations, lexical insertion – are not supported by the neural tissue of this cerebral region, nor is lexical or combinatorial semantics. The dense body of empirical evidence supporting this restrictive view comes mainly from several angles on lesion studies of syntax in agrammatic Broca's aphasia. Five empirical arguments are presented: experiments in sentence comprehension, cross-linguistic considerations (where aphasia findings from several language types are pooled and scrutinized comparatively), grammaticality and plausibility judgments, real-time processing of complex sentences, and rehabilitation. Also discussed are recent results from functional neuroimaging and from structured observations on speech production of Broca's aphasics. Syntactic abilities are nonetheless distinct from other cognitive skills and are represented entirely and exclusively in the left cerebral hemisphere. Although more widespread in the left hemisphere than previously thought, they are clearly distinct from other human combinatorial and intellectual abilities. The neurological record (based on functional imaging, split-brain and right-hemisphere-damaged patients, as well as patients suffering from a breakdown of mathematical skills) indicates that language is a distinct, modularly organized neurological entity. Combinatorial aspects of the language faculty reside in the human left cerebral hemisphere, but only the transformational component (or algorithms that implement it in use) is located in and around Broca's area.
Early Growth Response Gene 1–mediated Apoptosis Is Essential for Transforming Growth Factor β1–induced Pulmonary Fibrosis

Fibrosis and apoptosis are juxtaposed in pulmonary disorders such as asthma and the interstitial diseases, and transforming growth factor (TGF)-β1 has been implicated in the pathogenesis of these responses. However, the in vivo effector functions of TGF-β1 in the lung and its roles in the pathogenesis of these responses are not completely understood. In addition, the relationships between apoptosis and other TGF-β1–induced responses have not been defined. To address these issues, we targeted bioactive TGF-β1 to the murine lung using a novel externally regulatable, triple transgenic system. TGF-β1 produced a transient wave of epithelial apoptosis that was followed by mononuclear-rich inflammation, tissue fibrosis, myofibroblast and myocyte hyperplasia, and septal rupture with honeycombing. Studies of these mice highlighted the reversibility of this fibrotic response. They also demonstrated that a null mutation of early growth response gene (Egr)-1 or caspase inhibition blocked TGF-β1–induced apoptosis. Interestingly, both interventions markedly ameliorated TGF-β1–induced fibrosis and alveolar remodeling. These studies illustrate the complex effects of TGF-β1 in vivo and define the critical role of Egr-1 in the TGF-β1 phenotype. They also demonstrate that Egr-1–mediated apoptosis is a prerequisite for TGF-β1–induced fibrosis and remodeling.
Parental smoking, socioeconomic factors, and risk of invasive meningococcal disease in children: a population based case-control study

AIMS To investigate the effects of parental smoking, socioeconomic characteristics, and indoor environment on the risk of invasive meningococcal disease in children. METHODS Population based case-control study. A total of 68 incident cases of invasive meningococcal disease in children less than 15 years old were compared with 135 controls selected from the same school and matched for year of birth, sex, and place of residence. Information on exposures was obtained in interviews with parents. RESULTS Invasive meningococcal disease was strongly associated with parental smoking; rate ratios adjusted for socioeconomic factors were 3.5 (95% confidence interval 1.4–8.7) for smoking of mother, 3.2 (1.5–6.9) for smoking of father, and 2.7 (1.3–5.4) for every 20 cigarettes smoked at home on an average day. The risk of the disease was strongly inversely related to maternal education and, less strongly, to ownership of a car and of a weekend house, father's education, crowding, and the number of siblings, but these associations were reduced or eliminated in multivariate models. The type of heating and cooking (used as proxies for indoor air pollution) were not associated with the disease. CONCLUSION The risk of invasive meningococcal disease in children is strongly influenced by parental smoking and unfavourable socioeconomic circumstances.
Bio-Imaging of Colorectal Cancer Models Using Near Infrared Labeled Epidermal Growth Factor

Novel strategies that target the epidermal growth factor receptor (EGFR) have led to the clinical development of monoclonal antibodies, which treat metastatic colorectal cancer (mCRC) but only subgroups of patients with increased wild type KRAS and EGFR gene copy, respond to these agents. Furthermore, resistance to EGFR blockade inevitably occurred, making future therapy difficult. Novel bio-imaging (BOI) methods may assist in quantization of EGFR in mCRC tissue thus complementing the immunohistochemistry methodology, in guiding the future treatment of these patients. The aim of the present study was to explore the usefulness of near infrared-labeled EGF (EGF-NIR) for bio-imaging of CRC using in vitro and in vivo orthotopic tumor CRC models and ex vivo human CRC tissues. We describe the preparation and characterization of EGF-NIR and investigate binding, using BOI of a panel of CRC cell culture models resembling heterogeneity of human CRC tissues. EGF-NIR was specifically and selectively bound by EGFR expressing CRC cells, the intensity of EGF-NIR signal to background ratio (SBR) reflected EGFR levels, dose-response and time course imaging experiments provided optimal conditions for quantization of EGFR levels by BOI. EGF-NIR imaging of mice with HT-29 orthotopic CRC tumor indicated that EGF-NIR is more slowly cleared from the tumor and the highest SBR between tumor and normal adjacent tissue was achieved two days post-injection. Furthermore, images of dissected tissues demonstrated accumulation of EGF-NIR in the tumor and liver. EGF-NIR specifically and strongly labeled EGFR positive human CRC tissues while adjacent CRC tissue and EGFR negative tissues expressed weak NIR signals. This study emphasizes the use of EGF-NIR for preclinical studies. Combined with other methods, EGF-NIR could provide an additional bio-imaging specific tool in the standardization of measurements of EGFR expression in CRC tissues.
What Else is Revealed by Order-Revealing Encryption?

The security of order-revealing encryption (ORE) has been unclear since its invention. Dataset characteristics for which ORE is especially insecure have been identified, such as small message spaces and low-entropy distributions. On the other hand, properties like one-wayness on uniformly-distributed datasets have been proved for ORE constructions. This work shows that more plaintext information can be extracted from ORE ciphertexts than was previously thought. We identify two issues: First, we show that when multiple columns of correlated data are encrypted with ORE, attacks can use the encrypted columns together to reveal more information than prior attacks could extract from the columns individually. Second, we apply known attacks, and develop new attacks, to show that the leakage of concrete ORE schemes on non-uniform data leads to more accurate plaintext recovery than is suggested by the security theorems which only dealt with uniform inputs.
Nearly-Linear Time Algorithms for Preconditioning and Solving Symmetric, Diagonally Dominant Linear Systems

We present a randomized algorithm that on input a symmetric, weakly diagonally dominant $n$-by-$n$ matrix $A$ with $m$ nonzero entries and an $n$-vector $b$ produces an ${\tilde{x}} $ such that $\|{\tilde{x}} - A^{\dagger} {b} \|_{A} \leq \epsilon \|A^{\dagger} {b}\|_{A}$ in expected time $O (m \log^{c}n \log (1/\epsilon))$ for some constant $c$. By applying this algorithm inside the inverse power method, we compute approximate Fiedler vectors in a similar amount of time. The algorithm applies subgraph preconditioners in a recursive fashion. These preconditioners improve upon the subgraph preconditioners first introduced by Vaidya in 1990. For any symmetric, weakly diagonally dominant matrix $A$ with nonpositive off-diagonal entries and $k \geq 1$, we construct in time $O (m \log^{c} n)$ a preconditioner $B$ of $A$ with at most $2 (n - 1) + O ((m/k) \log^{39} n)$ nonzero off-diagonal entries such that the finite generalized condition number $\kappa_{f} (A,B)$ is at most $k$, for some other constant $c$. I.
‘Good genes as heterozygosity’: the major histocompatibility complex and mate choice in Atlantic salmon (Salmo salar)

According to the theory of mate choice based on heterozygosity, mates should choose each other in order to increase the heterozygosity of their offspring. In this study, we tested the ‘good genes as heterozygosity’ hypothesis of mate choice by documenting the mating patterns of wild Atlantic salmon (Salmo salar) using both major histocompatibility complex (MHC) and microsatellite loci. Specifically, we tested the null hypotheses that mate choice in Atlantic salmon is not dependent on the relatedness between potential partners or on the MHC similarity between mates. Three parameters were assessed: (i) the number of shared alleles between partners (x and y) at the MHC (Mxy), (ii) the MHC amino–acid genotypic distance between mates' genotypes (AAxy), and (iii) genetic relatedness between mates (rxy). We found that Atlantic salmon choose their mates in order to increase the heterozygosity of their offspring at the MHC and, more specifically, at the peptide–binding region, presumably in order to provide them with better defence against parasites and pathogens. This was supported by a significant difference between the observed and expected AAxy (p = 0.0486). Furthermore, mate choice was not a mechanism of overall inbreeding avoidance as genetic relatedness supported a random mating scheme (p = 0.445). This study provides the first evidence that MHC genes influence mate choice in fish.
Auditory Resting-State Network Connectivity in Tinnitus: A Functional MRI Study

The underlying functional neuroanatomy of tinnitus remains poorly understood. Few studies have focused on functional cerebral connectivity changes in tinnitus patients. The aim of this study was to test if functional MRI “resting-state” connectivity patterns in auditory network differ between tinnitus patients and normal controls. Thirteen chronic tinnitus subjects and fifteen age-matched healthy controls were studied on a 3 tesla MRI. Connectivity was investigated using independent component analysis and an automated component selection approach taking into account the spatial and temporal properties of each component. Connectivity in extra-auditory regions such as brainstem, basal ganglia/NAc, cerebellum, parahippocampal, right prefrontal, parietal, and sensorimotor areas was found to be increased in tinnitus subjects. The right primary auditory cortex, left prefrontal, left fusiform gyrus, and bilateral occipital regions showed a decreased connectivity in tinnitus. These results show that there is a modification of cortical and subcortical functional connectivity in tinnitus encompassing attentional, mnemonic, and emotional networks. Our data corroborate the hypothesized implication of non-auditory regions in tinnitus physiopathology and suggest that various regions of the brain seem involved in the persistent awareness of the phenomenon as well as in the development of the associated distress leading to disabling chronic tinnitus.
Stabilization of more general high-order nonholonomic systems within finite settling time

In this paper, the finite-time stabilization problem is investigated for a class of more general high-order nonholonomic systems with strong nonlinear drifts. By using finite-time Lyapunov stability theorem and adding a power integrator technique, a state feedback controller is obtained. Based on switching strategy to overcome the uncontrollability problem associated with x0(0) = 0, the uncertain closed-loop system states are regulated to zero in a finite time. An illustrative example is provided to demonstrate the effectiveness of the proposed controller.
NIST High Accuracy Reference Reflectometer-Spectrophotometer

A new reflectometer-spectrophotometer has been designed and constructed using state-of-the-art technology to enhance optical properties of materials measurements over the ultraviolet, visible, and near-infrared (UV-Vis-NIR) wavelength range (200 nm to 2500 nm). The instrument, Spectral Tri-function Automated Reference Reflectometer (STARR), is capable of measuring specular and diffuse reflectance, bidirectional reflectance distribution function (BRDF) of diffuse samples, and both diffuse and non-diffuse transmittance. Samples up to 30 cm by 30 cm can be measured. The instrument and its characterization are described.
Diffusion Tensor Magnetic Resonance Imaging of the Human Calf: Comparison Between 1.5 T and 3.0 T—Preliminary Results

Objectives:To compare diffusion tensor-magnetic resonance imaging (DT-MRI) of human calf muscles at 1.5 T and 3.0 T, and to measure a number of quantitative parameters to characterize diffusion anisotropy in organized muscle tissue using similar imaging parameters. Methods and Materials:After Institutional Review Board approval and informed consent, five healthy volunteers were studied. Imaging was performed on both 1.5 T and 3.0 T MR systems using the similar imaging protocol. Diffusion-sensitized single-shot spin-echo echo planar imaging pulse sequences were used to collect 2-dimensional images through the calf. Imaging was performed using b-values of 0, 300, 500, and 700 s/mm2. Image analyses and tensor calculations were performed offline using DT imaging studio (Johns Hopkins University, Baltimore, MD). The eigenvalues (λ1, λ2, λ3), trace of the diffusion tensor (Tr⟨D⟩), fractional anisotropy, relative anisotropy, and volume ratio were calculated in 3 different calf muscles (medial and lateral gastrocnemius and soleus). Signal-to-noise ratios (SNRs) were compared for both field strengths (1.5 T and 3.0 T), the different muscles and all b-values. A regression analysis was performed to look at within-subject effects (linear mixed effect model). Results:No significant differences were found between all quantitative measured DT-MRI parameters, b-values, and muscle groups at 3.0 T and 1.5 T (P = 0.105; P = 0.719). The mean of SNR on the 2 different field strengths (3.0:1.5 T) was 1.64, which was significantly different (P < 0.0001). Significant differences in SNR in all 3 muscles were found between sequences using b = 300 s/mm2 and 700 s/mm2 (P < 0.001; P = 0.006) and between sequences using b = 300 s/mm2 and 500 s/mm2 (P < 0.001; P = 0.03), and 500 s/mm2 and 700 s/mm2 (P = 0.005; P = 0.03), respectively, for medial gastrocnemius and soleus muscle. Conclusions:This study demonstrates useful parameters to perform DT-MRI at 1.5 T and 3.0 T. DT-MRI at 1.5 T and 3.0 T provide in vivo validation of quantitative structural analysis of human skleletal muscle.
The effects of adding xylanase, vitamin C and copper sulphate to wheat-based diets on broiler performance

1. The study used a 3 × 3 factorial design to evaluate the effects of 3 additives (none; vitamin C {250 mg/kg}; copper sulphate {250 mg/kg}) and 3 enzyme additions (none; Avizyme 1300 {Finnfeeds Ltd, 1 g/kg in food}; Avizyme 1310 {liquid spray, post-pelleting, 0.5 g/kg}). All experimental diets were mixed, heat-conditioned (80°C for 2 min) and pelleted. Copper sulphate (diets NCu; DCu; LCu) and Avizyme 1300 (diets DN; DC; DCu) were added during mixing. Vitamin C was sprayed at 10 ml per kg (diets NC; DC; LC) and the liquid enzyme was diluted 20-fold and sprayed at the same rate (diets LN; LC; LCu), post-pelleting. 2. Additive or enzyme addition did not significantly affect DM intake or liveweight gain (LWG). Enzyme addition improved gain:food ( P =0.014), AME:GE ( P <0.001), ileal apparent digestibility of DM ( P =0.008) and starch ( P <0.001), faecal apparent digestibility of starch, crude fat and NDF ( P =0.008; <0.001; <0.001 respectively) and reduced in vivo viscosity ( P <0.001). 3. Copper sulphate addition depressed gain:food ( P =0.047), AME:GE ( P =0.002), ileal apparent digestibility of starch ( P <0.001) and faecal apparent digestibility of starch ( P =0.003) and crude fat ( P <0.001) due to a negative additive × enzyme interaction when copper sulphate and dry enzyme were included together. 4. Vitamin C decreased in vivo viscosity by 20% but failed to have any effect on performance. Both enzyme forms gave similar improvements in performance in the absence of copper sulphate.
Clinical Practice and Epidemiology in Mental Health Long-term Consequences of Traumatic Experiences: an Assessment of Former Political Detainees in Romania

Background: Research has suggested that organized violence and torture have long-term psychological effects that persist throughout the lifespan. The present survey aimed at examining the prevalence of posttraumatic stress disorder (PTSD), and other disorders and symptoms, all present in old age, as long-term consequences of politically motivated violence in a comparison design.
'There's no smoke without fire': are male ex-partners perceived as more 'entitled' to stalk than acquaintance or stranger stalkers?

In a stalking scenario, the prior relationship between and the gender of stalker and victim were systematically manipulated in order to judge culpability and consequences for the persons involved. Written vignettes were presented to 168 participants who responded via seven Likert scales. Stalker-victim relationship had three levels: ex-partner, acquaintance and stranger. In accordance with the 'Just World' hypothesis (Lerner, 1980), the victim was judged as having greater responsibility for the stalking when their harasser was an ex-partner or a prior acquaintance rather than a stranger, and police intervention was felt to be most necessary when the stalker was a stranger. Sex of stalker and victim was manipulated, and the following comparisons proved significant: when the perpetrator was male, bodily injury to the victim was seen as more likely and police intervention as more necessary than when the perpetrator was female; and male victims were viewed as more responsible for the scenario and as possessing greater powers to alleviate it. The Just World hypothesis and gender stereotypes provide a plausible account for these findings. Future research should determine whether criminal convictions show similar biases towards convicting male and stranger stalkers more often than female and ex-partner stalkers.