Miracle-dz/UniFAR-FTUs huggingface dataset:
Fiber Tractography in Diffusion Tensor Magnetic Resonance Imaging: A Survey and Beyond

Diffusion tensor magnetic resonance imaging (DT-MRI) is the first noninvasive in vivo imaging modality with the potential to generate fiber tract trajectories in soft fibrous tissues, such as the brain white matter. Several newly developed fiber reconstruction and tractography techniques based on DT-MRI are reviewed in this article, including streamline fiber tracking techniques, diffusion tensor deflection strategy, probabilistic Monte-Carlo method, fast marching tractography based on level set principles, and diffusion simulation-based tractography. We also discuss some potential applications of DT-MRI fiber tractography and list a few available tractography and visualization software packages.
Identification of lncRNA‐155 encoded by MIR155HG as a novel regulator of innate immunity against influenza A virus infection

Long noncoding RNAs (lncRNAs) are single‐stranded RNA molecules longer than 200 nt that regulate many cellular processes. MicroRNA 155 host gene (MIR155HG) encodes the microRNA (miR)‐155 that regulates various signalling pathways of innate and adaptive immune responses against viral infections. MIR155HG also encodes a lncRNA that we call lncRNA‐155. Here, we observed that expression of lncRNA‐155 was markedly upregulated during influenza A virus (IAV) infection both in vitro (several cell lines) and in vivo (mouse model). Interestingly, robust expression of lncRNA‐155 was also induced by infections with several other viruses. Disruption of lncRNA‐155 expression in A549 cells diminished the antiviral innate immunity against IAV. Furthermore, knockout of lncRNA‐155 in mice significantly increased IAV replication and virulence in the animals. In contrast, overexpression of lncRNA‐155 in human cells suppressed IAV replication, suggesting that lncRNA‐155 is involved in host antiviral innate immunity induced by IAV infection. Moreover, we found that lncRNA‐155 had a profound effect on expression of protein tyrosine phosphatase 1B (PTP1B) during the infection with IAV. Inhibition of PTP1B by lncRNA‐155 resulted in higher production of interferon‐beta (IFN‐β) and several critical interferon‐stimulated genes (ISGs). Together, these observations reveal that MIR155HG derived lncRNA‐155 can be induced by IAV, which modulates host innate immunity during the virus infection via regulation of PTP1B‐mediated interferon response.
Survey for Galaxies Associated with z ~ 3 Damped Lyα Systems. I. Spectroscopic Calibration of u'BVRI Photometric Selection

We present a survey of z ~ 3 Lyman break galaxies (LBGs) associated with damped Lyα systems (DLAs) with the primary purpose of determining the DLA-LBG cross-correlation. This paper describes the acquisition and analysis of imaging and spectroscopic data of nine quasar fields having 11 known z ~ 3 DLAs covering an area of 465 arcmin2. Using deep u'BVRI images, 796 LBG candidates up to an apparent RAB magnitude of 25.5 were photometrically selected from 17,343 sources detected in the field. Spectroscopic observations of 529 LBG candidates using the Keck Low Resolution Imaging Spectrometer yielded 339 redshifts. We have conservatively identified 211 z > 2 objects with ⟨z⟩ = 3.02 ± 0.32. We discuss our method of z ~ 3 LBG identification and present a model of the u'BVRI photometric selection function. We use the 339 spectra to evaluate our u'BVRI z ~ 3 Lyman break photometric selection technique.
Normal Activity of Microsomal Triglyceride Transfer Protein Is Required for the Oleate-induced Secretion of Very Low Density Lipoproteins Containing Apolipoprotein B from McA-RH7777 Cells*

The requirement of the activity of microsomal triglyceride transfer protein (MTP) for very low density lipoprotein (VLDL) secretion was determined using McA-RH7777 cells stably transfected with human apoB48 (hB48). Secretion of VLDL containing hB48 (hB48-VLDL) by the transfected cells was induced by exogenous oleate (0.4 mm), and oleate-dependent VLDL secretion was selectively inhibited by brefeldin A (0.2 μg/ml). Two protocols were used to determine the effect of MTP inhibition on VLDL secretion. In the first protocol, cell protein and lipid were labeled with radioactive amino acids and oleate prior to MTP inhibition (using 5 μm of the photoaffinity inhibitor BMS-192951 to reduce MTP activity by 65–70%), and secretion of prelabeled apoB and triacylglycerol (TG) associated with lipoproteins was monitored during oleate-supplemented chase. In control cells, a 6-fold increase in incorporation of prelabeled TG into hB48-VLDL was observed after oleate supplement, while incorporation of prelabeled TG into VLDL containing endogenous rat apoB100 (rB100-VLDL) was unaffected. Inhibition of MTP activity abolished the oleate-induced utilization of prelabeled TG (by 80%) and hB48 (by 70%) for hB48-VLDL secretion but decreased utilization of pre-existing TG (by <25%) and B100 (by 45%) for rB100-VLDL secretion to a lesser extent. Inhibition of MTP did not affect incorporation of prelabeled TG or hB48 into high density lipoproteins containing hB48 (hB48-HDL). In the second protocol, MTP was inactivated prior to metabolic labeling of protein and lipid, and secretion of newly labeled apoB and TG as lipoproteins was monitored after oleate supplement. Under this condition, MTP inhibition decreased incorporation of newly labeled TG (by 80%) and hB48 (80%) into hB48-VLDL but did not affect their incorporation into hB48-HDL. Additionally, MTP inhibition decreased incorporation of newly labeled TG (by 50%) and rB100 (by 90%) into rB100-VLDL. Thus, normal activity of MTP is required for the oleate-induced secretion of hB48-VLDL from McA-RH7777 cells.
On Expected Accuracy

We empirically investigate the (negative) expected accuracy as an alternative loss function to cross entropy (negative log likelihood) for classification tasks. Coupled with softmax activation, it has small derivatives over most of its domain, and is therefore hard to optimize. A modified, leaky version is evaluated on a variety of classification tasks, including digit recognition, image classification, sequence tagging and tree tagging, using a variety of neural architectures such as logistic regression, multilayer perceptron, CNN, LSTM and Tree-LSTM. We show that it yields comparable or better accuracy compared to cross entropy. Furthermore, the proposed objective is shown to be more robust to label noise.
Electrophysiological and Psychophysical Studies of Meridional Anisotropies in Children With and Without Astigmatism.

Purpose We investigated the pattern of meridional anisotropies, if any, for pattern onset-offset visual evoked potential (POVEPs) responses and psychophysical grating acuity (GA) in children with normal letter visual acuity (20/20 or better). Methods A total of 29 children (aged 3-9 years), nine of whom were astigmatic (AS), were recruited. Orientation-specific monocular POVEPs were recorded in response to sinewave grating stimuli oriented along the subjects' principal AS meridians. Horizontal and vertical gratings were designated Meridians 1 and 2, respectively, for nonastigmatic patients (Non-AS). Binocular POVEPs in response to the same stimuli, but oriented at 45°, 90°, 135°, and 180°, were recorded. Psychophysical GAs were assessed monocularly and binocularly along the same meridians using the same stimuli by a 2-alternative-forced-choice staircase technique. The C3 amplitudes and peak latencies of the POVEP and GAs were compared across meridians using linear mixed models (monocular) and ANOVA (binocular). Results There were significant meridional anisotropies in monocular C3 amplitudes regardless of astigmatism status (P = 0.001): Meridian 2 (mean ± SE Non-AS, 30.13 ± 2.07 μV; AS, 26.53 ± 2.98 μV) was significantly higher than Meridian 1 (Non-AS, 26.14 ± 1.87 μV; AS, 21.68 ± 2.73 μV; P = 0.019), but no meridional anisotropies were found for GA or C3 latency. Binocular C3 amplitude in response to horizontally oriented stimuli (180°, 29.71 ± 3.06 μV) was significantly lower than the oblique (45°, 36.62 ± 3 .05 μV; P = 0.03 and 135°, 35.95 ± 2.92 μV; P = 0.04) and vertical (90°, 37.82 ± 3.65 μV; P = 0.02) meridians, and binocular C3 latency was significantly shorter in response to vertical than oblique gratings (P ≤ 0.001). Conclusions Meridional anisotropy was observed in children with normal vision. The findings suggest that horizontal gratings result in a small, but significantly lower POVEP amplitude than for vertical and oblique gratings.
Determinants of internal governance quality: Evidence from corporations in Ethiopia

Abstract The study analysed the factors that affect the internal governance quality of corporations in Ethiopia. It performed an ordered logistic regression analysis on a randomly selected sample of 76 corporations to analyse the effect of the ownership structure, form of ownership (private or government), leverage, corporate size, and sales growth on the internal governance quality score (IGQS). The governance quality score was measured using 20 indices categorized into four perspectives: disclosure, board characteristics, ethics, and shareholder rights. In this study, a significant positive effect of the corporate size and sales growth on the IGQS was found. In addition, government-owned corporations were found to perform better than privately owned corporations. It is recommended that appropriate authorities and officials should encourage the use of the corporate governance system in privately owned corporations and the convergence of internal governance quality of the two groups of corporations to the highest level.
Computer Science and Metaphysics: A Cross-Fertilization

Abstract Computational philosophy is the use of mechanized computational techniques to unearth philosophical insights that are either difficult or impossible to find using traditional philosophical methods. Computational metaphysics is computational philosophy with a focus on metaphysics. In this paper, we (a) develop results in modal metaphysics whose discovery was computer assisted, and (b) conclude that these results work not only to the obvious benefit of philosophy but also, less obviously, to the benefit of computer science, since the new computational techniques that led to these results may be more broadly applicable within computer science. The paper includes a description of our background methodology and how it evolved, and a discussion of our new results.
DNA energy constraints shape biological evolutionary trajectories

Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetrate themselves. Thus, the biological information contained within a dsDNA molecule, in terms of a linear sequence of nucleotides, has been considered the main target of the evolution. However, in this information-centred perspective, certain DNA sequence symmetries are difficult to explain. Here we show that these patterns can emerge from the physical peculiarities of the dsDNA molecule itself and the maximum entropy principle alone, rather than from biological or environmental evolutionary pressure. Our predictions are valid for both prokaryotes and eukaryotes, and also inform the interpretation of observed codon biases and context-dependent mutation patterns in human populations. Our results suggest that the double helix energy constraints and, more generally, the physical properties of the dsDNA are the hard drivers of the overall DNA sequence architecture, whereas the biological selective processes act as soft drivers, which only under extraordinary circumstances overtake the overall entropy content of the genome.
Tracking spatial modes in nearly hemispherical microcavities

We measure experimentally the spatial intensity profiles and resonant frequencies of the transverse modes of nearly hemi-spherical microcavities with cavity length and mirror curvatures below 10 mum. These resonators possess axially-symmetric Gauss-Laguerre-like modes, but do not display the frequency degeneracies typical of large-scale optical cavities. It is possible to interpret these results using a paraxial model of cavity propagation that includes non-parabolic optical elements.
Intimate partner violence and its associated factors among pregnant women in Bale Zone, Southeast Ethiopia: A cross-sectional study

Background Intimate partner violence (IPV) against women is a major public health concern in low income countries. Violence against pregnant women has adverse effects on maternal and newborn outcomes. This study aimed to assess the prevalence and associated factors of intimate partner violence in Southeast Ethiopia pregnant women. Methods Institutional based cross-sectional study was conducted on pregnant women who were attending antenatal care (ANC) in Bale Zone health institution during study period. Face to face interviews were conducted using a pre-tested structured questionnaire. Data related to socio-demographic characteristic, pregnancy and reproductive history, intimate partner behavior and IPV encountered during recent pregnancy was gathered for this study. Descriptive analysis and logistic regression were used for the data analysis. Odds ratio with 95% CI was computed to determine the presence and strength of associated factors with IPV. Results A total of 612 pregnant women participated in the study. Of these, 361 (59.0%) pregnant women faced at least one type of IPV during the recent pregnancy. Physical violence (20.3%), sexual violence (36.3%), psychological/emotional violence (33.0), controlling behavior violence (30.4%) and economic violence (27.0) were the type of IPV encountered by participants. An intimate partners who were drank alcohol [AOR = 2.9; 95% CI: (1.5–5.4)], partners who were chewed Khat [AOR = 1.7; 95% CI: (1.1–2.6)], partners who were smoked cigarette [AOR = 2.6; 95% CI: (1.4–4.9)], partners who had aggressive behavior [AOR = 2.8; 95% CI: (1.7–4.6)], having partner age ≥30 year old [AOR = 1.8; 95% CI: (1.2–2.9)], unwanted pregnancy [AOR = 3.3; 95% CI: (1.9–5.5)] and history of adverse pregnancy outcome [AOR = 2.1; 95% CI: (1.2–3.6)] that were the factors that significantly associated with IPV of the pregnant women. Conclusion The prevalence of IPV during pregnancy was high among the study participants. Intimate partners’ use of substance, intimate partners’ aggressive behavior, older intimate partners, unwanted pregnancy and history of adverse birth outcome were identified as associated factors for IPV. IPV needs to be considered during ANC service and integrated into the sexual and reproductive health education. Community-based interventions should be advocated as a way of health promotion. Counseling, awareness creation, service provision and program design on IPV is mandatory to minimize the victim.
Male clients of male sex workers in West Africa: A neglected high-risk population

Research on male clients of male sex workers (MCMSW) has been neglected for a long time globally. We aimed to characterize MCMSW and to identify factors associated with their sexual practices using data from the prospective cohort study CohMSM conducted in Burkina Faso, Côte d’Ivoire, Mali and Togo. Our study focused on HIV-negative men who have sex with other men (MSM) recruited between 06/2015 and 01/2018 by a team of trained peer educators. Scheduled study visits at 6, 12 and 18 months included medical examinations, HIV screening, risk-reduction counselling and face-to-face interviews to collect information on their sociodemographic characteristics, sexual behaviours, and HIV risk-reduction strategies (HIV-RRS). Three stigmatization sub-scores were constructed (experienced, perceived and internalized). Mixed-effects logistic regression was used for data analysis. Of the 280 participants recruited at baseline, 238, 211 and 118, respectively, had a follow-up visit at 6, 12 and 18 months. Over a total of 847 visits, 47 transactional sex (TS) encounters were reported by 38 MCMSW (13.6%). Of the latter, only one participant reported systematic TS (2.6%), 18 (47.4 %) stopped reporting TS after baseline, and 6 (15.8%) reported TS after baseline. Thirteen participants (34.2 %) reported occasional TS. After adjusting for country of study and age, the following self-reported factors were associated with a greater likelihood of being MCMSW: protected anal sex, exclusively insertive anal sex with male sexual partners, avoidance of sex after consuming psychoactive products and experiencing stigmatization (all during the previous 6 months). The majority of MCMSW in this study employed HIV-RRS with male sexual partners, including engaging in protected anal sex, avoidance of sex when consuming psychoactive products, and practising exclusively insertive anal sex.
Outcomes of Open Abdomen versus Primary Closure following Emergent Laparotomy for Suspected Secondary Peritonitis: A Propensity-Matched Analysis.

BACKGROUND Optimal management following index laparotomy is poorly defined in secondary peritonitis patients. Although "open abdomen" (OA), or temporary abdominal closure with planned relaparotomy, is utilized to reassess bowel viability or severity of contamination, recent studies demonstrate comparable morbidity and mortality with primary abdominal closure (PC). This study evaluates differences between OA and PC following emergent laparotomy. METHODS Using the Premier database at a quaternary care center (2012-2016), non-trauma patients with secondary peritonitis requiring emergent laparotomy were identified (N=534). Propensity-matching for PC (N=331;62%) or OA (N=203;38%) was performed using variables: Mannheim Peritonitis Index, lactate, and vasopressor requirement. 111 closely matched pairs (PC:OA) were compared. RESULTS 534 patients (55.0% female, mean age 59.6±15.5 years) underwent emergent laparotomy. Of OA patients, 136 (67.0%) had one relaparotomy, while 67 (33.0%) underwent multiple reoperations. Compared to daytime cases, laparotomies performed overnight (6pm-6am) had more temporary closures with OA (42.8% OA vs. 57.2% PC, p=0.04). When assessing by surgeon type, PC was performed in 78.7% of laparotomies by surgical subspecialties compared to 56.7% (p<0.0001) of acute care surgeons. After propensity-matching, OA patients had increased postoperative complications (71.2% vs. 41.4%, p<0.0001), mortality (22.5% vs. 11.7%, p=0.006), and longer median length of stay (LOS) (13 vs. 9 days, p=0.0001). CONCLUSIONS OA was performed in 38.0% of patients, with one-third of those requiring multiple reoperations. Complications, mortality rates and costs associated with OA were significantly increased when compared to PC. Given these findings, future studies are needed to determine appropriate indications for OA. LEVEL OF EVIDENCE Level III STUDY TYPE: Therapeutic/care management.
Blood pressure and heart rate predict outcome in patients acutely admitted with suspected myocarditis without previous heart failure

Objective: The study investigated the prognostic impact of blood pressure and heart rate in patients acutely admitted with suspected myocarditis without previous heart failure who underwent endomyocardial biopsy. Methods and results: In our prospectively planned study SBP, DBP, mean arterial blood pressure (MAP) and ECGs on admission were analyzed retrospectively in 175 patients with suspected myocarditis, who underwent endomyocardial biopsy between 1994 and 2007. Patients were followed up for a median of 53 ± 41 months, corresponding to a total follow-up of 9337 patient months. The primary endpoint was the time to cardiac death or heart transplantation, which occurred in 39 patients (22%). Baseline SBP was inversely associated with primary endpoint occurrence. Per 1 mmHg increase in SBP, the hazard ratio for the primary endpoint decreased by 4.3% [hazard ratio = 0.96, confidence interval (CI) = 0.94–0.98, P < 0.001]. The increased risk at a SBP below the mean value was confirmed after adjusting for the known independent predictors immunohistological signs of inflammation in biopsy samples, New York Heart Association functional class, and lack of &bgr;-blocker treatment (hazard ratio = 2.78, CI = 1.25–6.18, P = 0.012). In the presence of all risk predictors, hazard ratio for primary endpoint was 4.97 (CI = 2.28–10.83, P < 0.001). In a subgroup analysis of patients without &bgr;-blocker treatment, atrial fibrillation or pacemaker, a high heart rate was also associated with poor outcome (hazard ratio = 2.92, CI = 1.02–8.29, P = 0.045). Conclusion: In patients with suspected myocarditis without previous chronic heart failure low SBP, DBP and MAP were predictors of poor outcome. However, in patients not treated with &bgr;-blockers, a high heart rate was a predictor for cardiac death or heart transplantation.
Rapid Estrogen Receptor Signaling Is Essential for the Protective Effects of Estrogen Against Vascular Injury

Background— Clinical trial and epidemiological data support that the cardiovascular effects of estrogen are complex, including a mixture of both potentially beneficial and harmful effects. In animal models, estrogen protects females from vascular injury and inhibits atherosclerosis. These effects are mediated by estrogen receptors (ERs), which, when bound to estrogen, can bind to DNA to directly regulate transcription. ERs can also activate several cellular kinases by inducing a rapid nonnuclear signaling cascade. However, the biological significance of this rapid signaling pathway has been unclear. Methods and Results— In the present study, we develop a novel transgenic mouse in which rapid signaling is blocked by overexpression of a peptide that prevents ERs from interacting with the scaffold protein striatin (the disrupting peptide mouse). Microarray analysis of ex vivo treated mouse aortas demonstrates that rapid ER signaling plays an important role in estrogen-mediated gene regulatory responses. Disruption of ER-striatin interactions also eliminates the ability of estrogen to stimulate cultured endothelial cell migration and to inhibit cultured vascular smooth muscle cell growth. The importance of these findings is underscored by in vivo experiments demonstrating loss of estrogen-mediated protection against vascular injury in the disrupting peptide mouse after carotid artery wire injury. Conclusions— Taken together, these results support the concept that rapid, nonnuclear ER signaling contributes to the transcriptional regulatory functions of ER and is essential for many of the vasoprotective effects of estrogen. These findings also identify the rapid ER signaling pathway as a potential target for the development of novel therapeutic agents.