Miracle-dz/UniFAR-FTUs huggingface dataset:
Divide and conquer: A fast matrix inverse method of iterative adaptive approach for real beam superresolution

This paper present an efficient matrix inverse algorithm of the recent iterative adaptive approach (IAA) in the application of real beam superresolution (RBS). Based on the inherently band structure of the covariance matrix, the computational complexity of inverse can be reduced by avoiding the computation of zero elements. To achieve this, the divide and conquer (D&C) method will be introduced to fast inverse the covariance matrix. Numerical simulations illustrate the efficiency of the proposed algorithm.
Alternative Splicing of Differentiated Myeloid Cell Transcripts after Infection by Anaplasma phagocytophilum Impacts a Selective Group of Cellular Programs

Eukaryotic proteome diversity exceeds that encoded within individual genes, and results in part from alternative splicing events of pre-messenger RNA. The diversity of these splicing events can shape the outcome in development and differentiation of normal tissues, and is important in pathogenic circumstances such as cancer and some heritable conditions. A role for alternative splicing of eukaryotic genes in response to viral and intracellular bacterial infections has only recently been recognized, and plays an important role in providing fitness for microbial survival, while potentially enhancing pathogenicity. Anaplasma phagocytophilum survives within mammalian neutrophils by reshaping transcriptional programs that govern cellular functions. We applied next generation RNAseq to ATRA-differentiated HL-60 cells established to possess transcriptional and functional responses similar to A. phagocytophilum-infected human neutrophils. This demonstrated an increase in transcripts with infection and high proportion of alternatively spliced transcript events (ASEs) for which predicted gene ontology processes were in part distinct from those identified by evaluation of single transcripts or gene-level analyses alone. The alternative isoforms are not on average shorter, and no alternative splicing in genes encoding spliceosome components is noted. Although not evident at gene-level analyses, individual spliceosome transcripts that impact nearly all spliceosome components were significantly upregulated. How the distinct GO processes predicted by ASEs are regulated by infection and whether they are relevant to fitness or pathogenicity of A. phagocytophilum should be addressed in more detailed studies.
Mode-splitting of a non-polarizing guided mode resonance filter by substrate overetching effect

We investigate substrate overetch effect on resonance properties of sub-wavelength titanium oxide (TiO2) Guided Mode Resonance Filters (TiO2-GMRFs). The TiO2-GMRF is designed and fabricated to possess a non-polarizing behavior, which is strongly dependent on substrate (fused silica) overetch depth. For non-polarizing gratings at resonance, TE- and TM-modes have the same propagation constants. However, an overetch substrate effect results in splitting of the degenerate modes, which is studied theoretically and experimentally. The TiO2-SiO2 GMRFs are designed by Fourier Modal method (FMM) based on the rigorous calculation of electromagnetic diffraction theory at a designed wavelength of 850 nm. The TiO2-SiO2 gratings are fabricated by Atomic Layer Deposition (ALD), Electron Beam Lithography (EBL), and Reactive Ion Etching (RIE), and they are subsequently characterized structurally by Scanning Electron Microscopy (SEM) and optically by a spectroscopic ellipsometer. Several grating samples are fabricated by gradually increasing the overetch depth into fused silica and measuring the extent of TE- and TM-mode-splitting. A close agreement between the calculated and experimentally measured resonance wavelength spectral shift is found to describe the mode splitting of non-polarizing gratings.
Evaluation of contrasting techniques for X‐ray imaging of velvet worms (Onychophora)

Non‐invasive imaging techniques like X‐ray computed tomography have become very popular in zoology, as they allow for simultaneous imaging of the internal and external morphology of organisms. Nevertheless, the effect of different staining approaches required for this method on samples lacking mineralized tissues, such as soft‐bodied invertebrates, remains understudied. Herein, we used synchrotron radiation‐based X‐ray micro‐computed tomography to compare the effects of commonly used contrasting approaches on onychophorans – soft‐bodied invertebrates important for studying animal evolution. Representatives of Euperipatoides rowelli were stained with osmium tetroxide (vapour or solution), ruthenium red, phosphotungstic acid, or iodine. Unstained specimens were imaged using both standard attenuation‐based and differential phase‐contrast setups to simulate analyses with museum material. Our comparative qualitative analyses of several tissue types demonstrate that osmium tetroxide provides the best overall tissue contrast in onychophorans, whereas the remaining staining agents rather favour the visualisation of specific tissues and/or structures. Quantitative analyses using signal‐to‐noise ratio measurements show that the level of image noise may vary according to the staining agent and scanning medium selected. Furthermore, box‐and‐whisker plots revealed substantial overlap in grey values among structures in all datasets, suggesting that a combination of semiautomatic and manual segmentation of structures is required for comprehensive 3D reconstructions of Onychophora, irrespective of the approach selected. Our results show that X‐ray micro‐computed tomography is a promising technique for studying onychophorans and, despite the benefits and disadvantages of different staining agents for specific tissues/structures, this method retrieves informative data that may eventually help address evolutionary questions long associated with Onychophora.
Early intervention in Crohn’s disease: towards disease modification trials

Crohn’s disease (CD) is a chronic progressive destructive inflammatory bowel disease. As in rheumatoid arthritis, there is increasing evidence that early treatment initiation with disease-modifying agents, such as biological drugs, may lead to complete disease control, prevention of disease progression thus protecting against irreversible damage and restoration of normal quality of life. Data from randomised clinical trials with immunosuppressants and biologics suggest that treating patients with a disease duration of <2 years and an absence of complications may significantly reduce the risk for complications and increase time in remission in patients with CD. Moreover, rapid disease control may effectively prevent disease progression and allow dose reduction or even withdrawal of treatment, reducing the risk of long-term adverse events and healthcare costs. However, prospective disease modification trials are needed to confirm these initial results. Here we review the literature regarding early intervention in adult patients with CD and propose criteria for future disease modification trials.
Complex Magnetic Investigation of Ferritic Stainless Steel

Magnetic Barkhausen noise measurement (MBN) is a relatively new non-destructive detection technique. Its working principle is based on Barkhausen discontinuities or noise when a ferromagnetic material is subjected to a varying magnetic field. MBN is being used to characterise the stress state of a ferritic stainless steel (AISI 430). Other magnetic parameters such as saturation induction (BMax), remnant induction (BR), coercive field (HC) and maximal relative permeability (PMax) derived from the hysteresis loop have also been used to support the results achieved using MBN. Microstructural changes due to cold working and heat treatments were characterized by the applied magnetic measurements. The MBN technique was proved to be a useful non-destructive and quantitative method for microstuctural investigation of the investigated ferritic stainless steel.
5‐Methyltetrahydrofolate inhibits photosensitization reactions and strand breaks in DNA

The known functions of folate are to support one‐carbon metabolism and to serve as photoreceptors for cryptochromes and photolyases. We demonstrate that 5‐methyltetrahydrofolate (5‐MTHF, the predominant folate in plasma) is also a potent, near diffusion limited, scavenger of singlet oxygen and quencher of excited photosensitizers. Both pathways result in decomposition of 5‐MTHF, although ascor‐bate can protect against this loss. In the absence of photosensitizers, 5‐MTHF is directly decomposed only very slowly by UVA or UVB. Although synthetic folic acid can promote DNA damage by UVA, submicromo‐lar 5‐MTHF inhibits photosensitization‐induced strand breaks. These observations suggest a new role for reduced folate in protection from ultraviolet damage and have bearing on the hypothesis that folate photo‐degradation influenced the evolution of human skin color. –Offer, T. , Ames, B. N. , Bailey, S. W. , Sabens, E. A. , Nozawa, M. , Ayling, J. E. 5‐Methyltetrahydrofolate inhibits photosensitization reactions and strand breaks in DNA. FASEB J. 21, 2101–2107 (2007)
Effect of probiotic strain Lactobacillus acidophilus (LBKV-3) on fecal residual lactase activity in undernourished children below 10 years

ABSTRACT Clinically proven Lactobacillus acidophilus strain LBKV-3 intended as probiotic for humans was used to test its effect on fecal residual lactase activity in undernourished children below 10 years of age. The children were selected from malnutrition-declared area of Maharashtra (India). One of the major causes of malnutrition is lactose intolerance which leads to diarrhea. The basic consideration in selecting the probiotic strain of L. acidophilus (LBKV-3) in this investigation was the fact that the organism is isolated from human vaginal surface swab and it was found extensively studied for probiotic characteristic. LBKB3 is tested by several workers as probiotic for hypocholesterolemic activity, implantation ability, therapeutic effects on gastrointestinal (GI) and related ailments. The results of present investigation have shown that the fecal residual lactase activity significantly increased than its initial value (which was almost zero). It appeared that the fecal residual β-galactosidase activity is an indication of positive implementation abilities of the cultures under investigation. These trends were compared with the control and blank group of children receiving Dahi and buffalo milk (BM). It was observed that both these products failed to exert any significant impact on increase in residual lactase activity.
Speech Processing to Improve the Perception of Speech in Background Noise for Children With Auditory Processing Disorder and Typically Developing Peers

Auditory processing disorder (APD) may be diagnosed when a child has listening difficulties but has normal audiometric thresholds. For adults with normal hearing and with mild-to-moderate hearing impairment, an algorithm called spectral shaping with dynamic range compression (SSDRC) has been shown to increase the intelligibility of speech when background noise is added after the processing. Here, we assessed the effect of such processing using 8 children with APD and 10 age-matched control children. The loudness of the processed and unprocessed sentences was matched using a loudness model. The task was to repeat back sentences produced by a female speaker when presented with either speech-shaped noise (SSN) or a male competing speaker (CS) at two signal-to-background ratios (SBRs). Speech identification was significantly better with SSDRC processing than without, for both groups. The benefit of SSDRC processing was greater for the SSN than for the CS background. For the SSN, scores were similar for the two groups at both SBRs. For the CS, the APD group performed significantly more poorly than the control group. The overall improvement produced by SSDRC processing could be useful for enhancing communication in a classroom where the teacher’s voice is broadcast using a wireless system.
Alpha-1 Antitrypsin Deficiency Detection in a Portuguese Population

ABSTRACT Alpha-1 antitrypsin deficiency (AATD) is an autosomal co-dominant disease characterised by low serum levels of this molecule. Its epidemiology remains unknown in many countries, mainly due to its underdiagnosed state and lack of patients’ registries. We aim to evaluate and characterise a sample of Portuguese individuals tested for AATD, between 2006 and 2015, based on a retrospective analysis from the database of a laboratory offering AATD genetic diagnosis service. 1684 individuals were considered, covering almost every region in Portugal. Genetic diagnosis resulted from requests of clinicians from different areas of expertise, mainly pulmonology (35.5%). Most subjects could be distributed into more common genotypes: MZ (25.4%, n = 427), MS (15.5%, n = 261), SZ (11.2%, n = 188), ZZ (9.4%, n = 158) and SS (5.6%, n = 95). 9.5% of the subjects were found to carry at least one rare deleterious allele, including the recently described PGaia, Q0Oliveira do Douro, Q0Vila Real and a novel SGaia variant. This study comprises 417 subjects (24.7%) with severe to very severe AATD and 761 carriers (45.2%), 22.7% of those identified by familial screening. The present study represents the most complete survey of AATD in Portugal so far and discloses a high rate of severe and very severe deficiency cases, attributed not only to ZZ and SZ genotypes but also to a large number of rare combinations with other null and deficiency alleles. It also uncovers a low awareness to AATD among the medical community, highlighting the need to create a Portuguese national registry and AATD guidelines and increase the awareness about this condition.
Placental development and function in women with a history of placenta‐related complications: a systematic review

Women with a history of placenta‐related pregnancy complications, such as preeclampsia, intrauterine growth restriction or preterm delivery, have an increased risk for recurrence of such complications. This recurrence is likely the result of underlying endothelial dysfunction that leads to abnormal placentation, especially in complications with an early onset. This study provides an overview of biomarkers of placental development and function in pregnancies from women with a history of placenta‐related complications.
T-Crowd: Effective Crowdsourcing for Tabular Data

We study the effective use of crowdsourcing in filling missing values in a given relation (e.g., a table containing different attributes of celebrity stars, such as nationality and age). A task given to a worker typically consists of questions about the missing attribute values (e.g., what is the age of Jet Li? ). Existing work often treats related attributes independently, leading to suboptimal performance. We present T-Crowd: a crowdsourcing system that considers attribute relationships. T-Crowd integrates each worker's answers on different attributes to effectively learn his/her trustworthiness and the true data values. Our solution seamlessly supports categorical and continuous attributes. Our experiments on real datasets show that T-Crowd outperforms state-of-the-art methods, improving the quality of truth inference.
Closing the loop with an enhanced referral management system

Objective To evaluate the impact of a referral manager tool on primary care practices. Materials and Methods We evaluated a referral manager module in a locally developed electronic health record (EHR) that was enhanced to improve the referral management process in primary care practices. Baseline (n = 61) and follow-up (n = 35) provider and staff surveys focused on the ease of performing various steps in the referral process, confidence in completing those steps, and user satisfaction. Additional metrics were calculated that focused on completed specialist visits, acknowledged notes, and patient communication. Results Of 1341 referrals that were initiated during the course of the study, 76.8% were completed. All the steps of the referral process were easier to accomplish following implementation of the enhanced referral manager module in the EHR. Specifically, tracking the status of an in-network referral became much easier (+1.43 [3.91-2.48] on a 5-point scale, P < .0001). Although we found improvement in the ease of performing out-of-network referrals, there was a greater impact on in-network referrals. Discussion Implementation of an electronic tool developed using user-centered design principles along with adequate staff to monitor and intervene when necessary made it easier for primary care practices to track referrals and to identify if a breakdown in the process occurred. This is especially important for high-priority referrals. Out-of-network referrals continue to present challenges, which may eventually be helped by improving interoperability among EHRs and scheduling systems. Conclusion An enhanced referral manager system can improve referral workflows, leading to enhanced efficiency and patient safety and reduced malpractice risk.
Regulation of brachyury by fibroblast growth factor receptor 1 in lung cancer

Recent evidence suggests that T-box transcription factor brachyury plays an important role in lung cancer development and progression. However, the mechanisms underlying brachyury-driven cellular processes remain unclear. Here we found that fibroblast growth factor receptor 1/mitogen-activated protein kinase (FGFR1/MAPK) signaling regulated brachyury in lung cancer. Analysis of FGFR1-4 and brachyury expression in human lung tumor tissue and cell lines found that only expression of FGFR1 was positively correlated with brachyury expression. Specific knockdown of FGFR1 by siRNA suppressed brachyury expression and epithelial–mesenchymal transition (EMT) (upregulation of E-cadherin and β-catenin and downregulation of Snail and fibronectin), whereas forced overexpression of FGFR1 induced brachyury expression and promoted EMT in lung cancer cells. Activation of fibroblast growth factor (FGF)/FGFR1 signaling promoted phosphorylated MAPK extracellular signal-regulated kinase (ERK) 1/2 translocation from cytoplasm to nucleus, upregulated brachyury expression, and increased cell growth and invasion. In addition, human lung cancer cells with higher brachyury expression were more sensitive to inhibitors targeting FGFR1/MAPK pathway. These findings suggest that FGFR1/MAPK may be important for brachyury activation in lung cancer, and this pathway may be an appealing therapeutic target for a subset of brachyury-driven lung cancer.
Message ordering in a multicast environment

Three ordering properties are characterized, namely, single-source, multiple-source, and multiple-group ordering, and their solutions are discussed. The multiple-group ordering property, which guarantees that two messages destined to two processes are delivered in the same relative order, even if they originate at different sources and are addressed to different multicast groups, is concentrated on. A protocol that solves the multiple-group ordering problem is presented. The issues of performance and reliability are addressed by providing comparisons with other techniques for ordering multicasts. In many cases this new algorithm solves the problem with greater efficiency than previous solutions without sacrificing reliability. It is pointed out that one disadvantage of the technique is that sometimes sites are required to handle messages which they do not need to deliver locally. These so-called extra nodes, however, do not occur frequently according to the experiments presented. <<ETX>>
A meta-analysis of the effects of measuring theory of planned behaviour constructs on behaviour within prospective studies

Measurement reactivity effects, such as the mere measurement effect, have been proposed as a reason for behavioural changes in a number of theory of planned behaviour intervention studies. However, it is unclear whether such changes are the result of the mere measurement effect or of other artefacts of intervention study design. The aim of this study is to determine the size and direction of changes in health behaviours from baseline to follow-up in prospective studies using the theory of planned behaviour. Electronic databases were searched for the theory of planned behaviour studies which measured health behaviours at two or more time points. Change in behaviour was calculated for all studies. Sixty-six studies were included. Mean effect sizes across all studies were small and negative (d = −.03). Effect size was moderated by behaviour, behaviour type and follow-up length. Subgroup analyses showed significant decreases in socially undesirable behaviour (d = −.28), binge drinking (d = −.17), risk driving (d = −.20), sugar snack consumption (d = −.43) and sun-protective behaviour (d = −.18). Measurement of intention at baseline resulted in significant decreases in undesirable behaviour. Changes in undesirable behaviours reported in other studies may be the result of the mere measurement effect.
Negative cognitive style and cortisol recovery accentuate the relationship between life stress and depressive symptoms

Abstract When exposed to stressful life events, a significant number of adolescents will experience depressive symptoms. One model of depression suggests that individuals with a negative cognitive style are most vulnerable to depression following life stress. Alternatively, altered activation of the hypothalamic–pituitary–adrenal axis may explain vulnerability to depression following life stress. Each of these models plausibly explains the emergence of depressive symptoms during adolescence and have been investigated largely independently. The current study recruited a sample of urban adolescents (N = 179) to evaluate whether cortisol response to a laboratory stress induction and negative cognitive style are related and whether they independently interact with exposure to stressful life events to predict symptoms of depression. Negative cognitive style was not associated with cortisol response to the laboratory stressor. Rather, negative cognitive style and cortisol recovery independently interacted with stressful life events to predict current symptoms of depression. Results support a heterogeneous etiology of depression.
Cognitive behavioral therapy for anxiety and related disorders: A meta‐analysis of randomized placebo‐controlled trials

The purpose of this study was to examine the efficacy of cognitive behavioral therapy (CBT) for anxiety‐related disorders based on randomized placebo‐controlled trials. We included 41 studies that randomly assigned patients (N = 2,843) with acute stress disorder, generalized anxiety disorder (GAD), obsessive compulsive disorder (OCD), panic disorder (PD), posttraumatic stress disorder (PTSD), or social anxiety disorder (SAD) to CBT or a psychological or pill placebo condition. Findings demonstrated moderate placebo‐controlled effects of CBT on target disorder symptoms (Hedges’ g = 0.56), and small to moderate effects on other anxiety symptoms (Hedges’ g = 0.38), depression (Hedges’ g = 0.31), and quality of life (Hedges’ g = 0.30). Response rates in CBT compared to placebo were associated with an odds ratio of 2.97. Effects on the target disorder were significantly stronger for completer samples than intent‐to‐treat samples, and for individuals compared to group CBT in SAD and PTSD studies. Large effect sizes were found for OCD, GAD, and acute stress disorder, and small to moderate effect sizes were found for PTSD, SAD, and PD. In PTSD studies, dropout rates were greater in CBT (29.0%) compared to placebo (17.2%), but no difference in dropout was found across other disorders. Interventions primarily using exposure strategies had larger effect sizes than those using cognitive or cognitive and behavioral techniques, though this difference did not reach significance. Findings demonstrate that CBT is a moderately efficacious treatment for anxiety disorders when compared to placebo. More effective treatments are especially needed for PTSD, SAD, and PD.