Miracle-dz/UniFAR-FTUs huggingface dataset:
HCV infection induces a unique hepatic innate immune response associated with robust production of type III interferons.

BACKGROUND & AIMS Polymorphisms in the IL28B gene have been associated with clearance of hepatitis C virus (HCV), indicating a role for type III interferons (IFNs) in HCV infection. Little is known about the function of type III IFNs in intrinsic antiviral innate immunity. METHODS We used in vivo and in vitro models to characterize the role of the type III IFNs in HCV infection and analyzed gene expression in liver biopsy samples from HCV-infected chimpanzees and patients. Messenger RNA and protein expression were studied in HCV-infected hepatoma cell lines and primary human hepatocytes. RESULTS HCV infection of primary human hepatocytes induced production of chemokines and type III IFNs, including interleukin (IL)-28, and led to expression of IFN-stimulated genes (ISGs). Chimpanzees infected with HCV showed rapid induction of hepatic type III IFN, associated with up-regulation of ISGs and minimal induction of type I IFNs. In liver biopsy specimens from HCV-infected patients, hepatic expression of IL-28 correlated with levels of ISGs but not of type I IFNs. HCV infection produced extensive changes with gene expression in addition to ISGs in primary human hepatocytes. The induction of type III IFNs is regulated by IFN regulatory factor 3 and nuclear factor κB. Type III IFNs up-regulate ISGs with a different kinetic profile than type 1 IFNs and induce a distinct set of genes, which might account for their functional differences. CONCLUSIONS HCV infection results predominantly in induction of type III IFNs in livers of humans and chimpanzees; the level of induction correlates with hepatic levels of ISGs. These findings might account for the association among IL-28, level of ISGs, and recovery from HCV infection and provide a therapeutic strategy for patients who do not respond to IFN therapy.
Histological and Functional Benefit Following Transplantation of Motor Neuron Progenitors to the Injured Rat Spinal Cord

Background Motor neuron loss is characteristic of cervical spinal cord injury (SCI) and contributes to functional deficit. Methodology/Principal Findings In order to investigate the amenability of the injured adult spinal cord to motor neuron differentiation, we transplanted spinal cord injured animals with a high purity population of human motor neuron progenitors (hMNP) derived from human embryonic stem cells (hESCs). In vitro, hMNPs displayed characteristic motor neuron-specific markers, a typical electrophysiological profile, functionally innervated human or rodent muscle, and secreted physiologically active growth factors that caused neurite branching and neuronal survival. hMNP transplantation into cervical SCI sites in adult rats resulted in suppression of intracellular signaling pathways associated with SCI pathogenesis, which correlated with greater endogenous neuronal survival and neurite branching. These neurotrophic effects were accompanied by significantly enhanced performance on all parameters of the balance beam task, as compared to controls. Interestingly, hMNP transplantation resulted in survival, differentiation, and site-specific integration of hMNPs distal to the SCI site within ventral horns, but hMNPs near the SCI site reverted to a neuronal progenitor state, suggesting an environmental deficiency for neuronal maturation associated with SCI. Conclusions/Significance These findings underscore the barriers imposed on neuronal differentiation of transplanted cells by the gliogenic nature of the injured spinal cord, and the physiological relevance of transplant-derived neurotrophic support to functional recovery.
A 240mW 2.1GS/s 12b pipeline ADC using MDAC equalization

This paper introduces MDAC equalization, a digital correction technique for pipeline ADCs that corrects MDAC gain and settling errors using successive digital FIR filters operating on sub-ADC output samples. This technique reduces the required MDAC residue amplifier (RA) bandwidth relative to the sampling frequency, thereby reducing ADC power. MDAC equalization is demonstrated in a 240mW 2.1GS/s 12b ping-pong pipeline ADC in 40nm CMOS where MDAC RA power is reduced from 175mW to 53mW by 70%.
Arithmetic structures in random sets

We extend two well-known results in additive number theory, Sarkozy’s theorem on square differences in dense sets and a theorem of Green on long arithmetic progressions in sumsets, to subsets of random sets of asymptotic density 0. Our proofs rely on a restriction-type Fourier analytic argument of Green and Green-Tao.
Identification of a Dehydrogenase Required for Lactose Metabolism in Caulobacter crescentus

ABSTRACT Caulobacter crescentus, which thrives in freshwater environments with low nutrient levels, serves as a model system for studying bacterial cell cycle regulation and organelle development. We examined its ability to utilize lactose (i) to gain insight into the metabolic capacities of oligotrophic bacteria and (ii) to obtain an additional genetic tool for studying this model organism, aiming to eliminate the basal enzymatic activity that hydrolyzes the chromogenic substrate 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-gal). Using a previously isolated transposon mutant, we identified a gene, lacA, that is required for growth on lactose as the sole carbon source and for turning colonies blue in the presence of X-gal. LacA, which contains a glucose-methanol-choline (GMC) oxidoreductase domain, has homology to the flavin subunit of Pectobacterium cypripedii's gluconate dehydrogenase. Sequence comparisons indicated that two genes near lacA, lacB and lacC, encode the other subunits of the membrane-bound dehydrogenase. In addition to lactose, all three lac genes are involved in the catabolism of three other β-galactosides (lactulose, lactitol, and methyl-β-d-galactoside) and two glucosides (salicin and trehalose). Dehydrogenase assays confirmed that the lac gene products oxidize lactose, salicin, and trehalose. This enzymatic activity is inducible, and increased lac expression in the presence of lactose and salicin likely contributes to the induction. Expression of lacA also depends on the presence of the lac genes, implying that the dehydrogenase participates in induction. The involvement of a dehydrogenase suggests that degradation of lactose and other sugars in C. crescentus may resemble a proposed pathway in Agrobacterium tumefaciens.
Statistical characterization of UWB propagation channel in ship cabin environment

This paper presents a statistical characterization of Ultra-Wideband (UWB) channel for ship cabin environment based on measurements carried out in the frequency-domain and covered the frequency band of 6-9GHz. According to the results of measurement, it is observed that rays arrive in clusters, so we describe the multipath propagation with the classical S-V model. The main purpose is to study multipath propagation behavior, particularly the phenomenon of clustered multipath components. An efficient cluster automatic identification algorithm based on wavelet analysis is employed for clusters identification of the discrete UWB channel impulse responses (CIRs). Then, the statistical characterizations of multi-path components (MPCs) are examined. Finally, simulation results of the proposed statistical model are compared to measured data demonstrating reasonable agreement. The results are helpful to model the UWB propagation channel in such environment.
Established and emerging coronary risk factors in patients with heterozygous familial hypercholesterolaemia

Objectives: To assess the clinical and biochemical factors associated with inter-individual variation in susceptibility to coronary artery disease (CAD) in treated heterozygous familial hypercholesterolaemia. Design: A cross sectional study was conducted of 410 patients recruited from six lipid clinics in the UK. Results: CAD was documented in 104 of the 211 men and in 55 of the 199 women with mean ages of onset of 43.1 and 46.5 years, respectively. CAD was significantly more common in men (49% v 28%, p < 0.001) and in patients who had smoked cigarettes versus patients who had never smoked (51% v 28%, p < 0.001). After adjusting for age, sex, and current smoking status, there were no significant differences between patients with or without CAD in lipoprotein(a), homocysteine, fibrinogen, plasminogen activator inhibitor-1, white blood cell count, body mass index, glucose, triglyceride or total cholesterol. However, high density lipoprotein (HDL) cholesterol concentrations were significantly lower in those with CAD (6%, 95% confidence interval (CI) 1% to 11%, p = 0.03) and this difference was greater in women than men (12% v 2%, p = 0.041). Conclusions: These results indicate that emerging coronary risk factors appear not to be associated with CAD in adults with treated familial hypercholesterolaemia, but the strong association with smoking suggests that patients should be identified early in childhood and discouraged from ever starting to smoke.
Technology-mediated information sharing between patients and clinicians in primary care encounters

Objective: The aim of this study was to identify and describe the use of electronic health records (EHRs) for information sharing between patients and clinicians in primary-care encounters. This topic is particularly important as computers and other technologies are increasingly implemented in multi-user health-care settings where interactions and communication between patients and clinicians are integral to interpersonal and organisational outcomes. Method: An ethnographic approach was used to classify the encounters into distinct technology-use patterns based on clinicians’ interactions with the technology and patients. Each technology-use pattern was quantitatively analysed to assist with comparison. Quantitative analysis was based on duration of patient and clinician gaze at EHR. Findings: Physicians employed three different styles to share information using EHRs: (1) active information sharing, in which a clinician turns the monitor towards the patient and uses the computer to actively share information with the patient; (2) passive information sharing, when a clinician does not move the monitor, but the patient might see the monitor by leaning in if they choose and (3) technology withdrawal, when a clinician does not share the monitor with the patient. Conclusion: A variety of technology-mediated information-sharing styles may be effective in providing patient-centred care. New EHR designs may be needed to facilitate information sharing between patients and clinicians.
PDCD1 genes may protect against extraocular manifestations in Chinese Han patients with Vogt-Koyanagi-Harada syndrome

Purpose To analyze the potential association of programmed cell death 1 (PDCD1) with Vogt-Koyanagi-Harada (VKH) syndrome in a Chinese Han population. Methods Three single nucleotide polymorphism (SNPs), PD-1.3G/A, PD-1.5C/T, and PD-1.6G/A, were genotyped in 247 VKH patients and 289 age-, sex-, and ethnically-matched healthy controls using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The associations of genotypes and alleles with VKH syndrome were analyzed. Results All genotype distributions in healthy controls were in Hardy–Weinberg equilibrium. The genotype and allele frequencies of PD-1.3, PD-1.5, and PD-1.6 were not different between patients with VKH syndrome and healthy controls. No significant difference was observed according to the status of human leukocyte antigen (HLA)-DR4 and HLA-DRw53. Compared to the controls, lower frequencies of the PD-1.5C genotype and allele frequencies were observed in VKH patients with extraocular findings. Conclusions PD-1.3 and PD-1.6 polymorphisms are not associated with the susceptibility to VKH syndrome in the Chinese Han population. However, PD-1.5 may be negatively associated with the occurrence of extraocular manifestations of VKH syndrome.
Lived Experiences of Women with Hidden Disabilities: A Phenomenologically Based Study

iii SIGNATURE PAGE v DEDICATION PAGE vi ACKNOWLEDGEMENTS vii LIST OF TABLES viii CHAPTER I: THE RESEARCH PROBLEM . 1 Statement of the Problem 1 Women with Disabilities 2 Invisible Disabilities . 4 Background and Need for the Study 7 The Social Model of Disability 7 Purpose of the Study 11 Research Questions 11 Theoretical Framework 12 Critical Disability Theory 12 Material Feminism 13 Phenomenology 15 Significance 16 Definition of Terms 17 CHAPTER II: THE REVIEW OF THE LITERATURE 19 Overview 19 The Disability Paradigm 19 Critiques of the Social Model of Disability 23 Introduction 23 Primary Lacuna in the Social Model of Disability 23 Alternatives to the Social Model of Disability 25 Experiences of Women with Physical Disabilities 28 Embodiment 28 Sites of Resistance and Acquiescence 29 Challenges for Women with Hidden (Non-Visible) Disabilities 31 Passing 33 Legitimacy 34 Discussion and Conclusion 40 CHAPTER III: METHODOLOGY 42 Restatement of the Purpose of the Study 42
Pulsed Sagnac polarization-entangled photon source with a PPKTP crystal at telecom wavelength

We demonstrate pulsed polarization-entangled photons generated from a periodically poled KTiOPO<sub>4</sub> (PPKTP) crystal in a Sagnac interferometer configuration at telecom wavelength. We achieved fidelities of 0.981 ± 0.0002 for |ψ<sup>-</sup>〉 and 0.980 ± 0.001 for |ψ<sup>+</sup>〉 respectively.
Villous Adenoma Coexisting with Non-Muscle Invasive Urothelial Carcinoma of the Bladder, Case Report

A 72-year old patient was admitted to hospital with the complaint of non-coagulated hematuria and pain. There was no remarkable finding in physical examination. Cystoscopic examination revealed two papillary tumors in the urinary bladder. Larger one measuring 25 mm was on the dome of bladder and the other was 16 mm mass in the left wall of urinary bladder, with enhancement. Cold punch biopsy was performed at cystoscopic examination. Histopathology confirmed that the resected one tumor was a villous adenoma, and the other was non-muscle invasive urothelial carcinoma. TUR was performed after punch biopsy. Each tumor was resected and diagnosed, respectively. Histopathology confirmed that the mass was a villous adenoma with a polypoid growth of the glandular epithelium consisting of small tubular glands, dilated cystic glands or papillary fronds lined by a columnar epithelium and including goblet cells. Intracellular and extracellular mucin was seen. Epithelial cells displayed mild nuclear atypia and nuclear pseudostratification suggestive of severe dysplasia. No invasive component was found in the villous adenoma (Figure 1). Immunohistochemical analysis of the polypoid lesion showed that the epithelial cells were diffusely positive for cytokeratin 20 (CK20), focally positive for cytokeratin 7 (CK7), carcinoembryonic antigen (CEA) and mucin 2 (MUC2). Non-muscle invazive urothelial carcinoma was identified the other side of urinary bladder (Figure 2). Based on the pathological findings, the patient was diagnosed with a rare case of villous adenoma of the bladder and non-muscle infiltrative urothelial carcinoma arising in the bladder. After BCG therapy, he has been followed by cystoscopic examination for every three months. Over the past 29 months of follow up no local recurrences were detected. 1Akdeniz University Faculty of Medicine, Department of Pathology, Antalya, Turkey 2Başkent University Faculty of Medicine, Department of Pathology, Antalya, Turkey 3Akdeniz University Faculty of Medicine, Department of Urology, Antalya, Turkey Bahar Akkaya MD1, Gülden Tasova-Yılmaz MD1, Hampar Akkaya MD2, Mustafa Faruk Usta MD3 Kas İnvazyonu Göstermeyen İnvaziv Ürotelial Karsinomla Birlikte Görülen Mesanenin Villöz Adenomu, Olgu Sunumu Villous Adenoma Coexisting with Non-Muscle Invasive Urothelial Carcinoma of the Bladder, Case Report
Spontaneous and evoked high‐frequency oscillations in the tetanus toxin model of epilepsy

Purpose: High‐frequency oscillations (HFOs) are an emerging biomarker for epileptic tissue. Yet the mechanism by which HFOs are produced is unknown, and their rarity makes them difficult to study. Our objective was to examine the occurrence of HFOs in relation to action potentials (APs) and the effect of microstimulation in the tetanus toxin (TT) model of epilepsy, a nonlesional model with a short latency to spontaneous seizures.
Big Bounce Genesis and Possible Experimental Tests: A Brief Review

We review the recent status of big bounce genesis as a new possibility of using dark matter particles’ mass and interaction cross-section to test the existence of a bounce universe at the early stage of evolution in our currently-observed universe. To study the dark matter production and evolution inside the bounce universe, called big bounce genesis for short, we propose a model independent approach. We shall present the motivation for proposing big bounce, as well as the model independent predictions, which can be tested by dark matter direct searches. A positive finding shall have profound impact on our understanding of the early universe physics.
Autologous Bone Marrow–Derived Cell Therapy in Patients With Critical Limb Ischemia: A Meta-Analysis of Randomized Controlled Clinical Trials

Background: Critical Limb Ischemia (CLI) is the most advanced stage of peripheral arterial disease and is usually treated with bypass surgery or endovascular revascularization. However, a considerable proportion of CLI patients are not eligible to these treatment strategies and amputation is often the only option left. In the past decade, research has focused on bone marrow (BM)–derived cell-based strategies that aim at neovascularization to improve limb perfusion. Individual studies did not convincingly prove efficacy of BM-derived cell therapy in CLI patients thus far. Objectives: Perform a meta-analysis of all randomized controlled trials (RCTs) available that studied BM-derived cell therapy compared to standard care with or without placebo in CLI patients and provide summary efficacy data on this approach. Methods: A systematic search in the electronic databases of Medline, Embase, and the Cochrane Controlled Trials Register was performed. All studies were critically appraised and data were extracted and meta-analyzed using a random-effects model. Major amputation and amputation-free survival were considered as the primary endpoints. Results: A total of 12 RCTs jointly including 510 CLI patients were identified and analyzed. The meta-analysis showed beneficial effects of BM-derived cell therapy on both subjective and surrogate objective endpoints, that is, pain score, pain-free walking distance, ankle-brachial index, and transcutaneous oxygen measurements (all P < 0.00001). Overall, the RCTs showed reduced amputation rates in the therapeutic arms of the included trials with a relative risk (RR) on major amputation of 0.58 [95% confidence interval (CI), 0.40–0.84; P = 0.004]. However, when only the placebo-controlled RCTs were considered, the beneficial effect on major amputation rates was considerably reduced and nonsignificant (RR = 0.78; 95% CI, 0.40–1.51; P = 0.46). Amputation-free survival did not significantly differ between the BM treated and the control group (RR = 1.16; 95% CI, 0.92–1.48; P = 0.22). Conclusions: This meta-analysis underlines the promising potential of BM-derived cell therapy in CLI patients. Importantly, the results of placebo-controlled and non–placebo-controlled RCTs seem to diverge, which stresses the necessity to use placebo in the control arms of these trials. Future well-designed larger placebo-controlled RCTs are needed and should include long-term follow-up data to assess durability of treatment effects.
Once More with Feeling: Supportive Responses to Social Sharing on Facebook

Life is more than cat pictures. There are tough days, heartbreak, and hugs. Under what contexts do people share these feelings online, and how do their friends respond? Using millions of de-identified Facebook status updates with poster-annotated feelings (e.g., “feeling thankful” or “feeling worried”), we examine the magnitude and circumstances in which people share positive or negative feelings and characterize the nature of the responses they receive. We find that people share greater proportions of both positive and negative emotions when their friend networks are smaller and denser. Consistent with social sharing theory, hearing about a friend's troubles on Facebook causes friends to reply with more emotional and supportive comments. Friends' comments are also more numerous and longer. Posts with positive feelings, on the other hand, receive more likes, and their comments have more positive language. Feelings that relate to the poster's self worth, such as “feeling defeated,” “feeling unloved,” or “feeling accomplished” amplify these effects.
Primary Differentiation in the Human Blastocyst: Comparative Molecular Portraits of Inner Cell Mass and Trophectoderm Cells

The primary differentiation event during mammalian development occurs at the blastocyst stage and leads to the delineation of the inner cell mass (ICM) and the trophectoderm (TE). We provide the first global mRNA expression data from immunosurgically dissected ICM cells, TE cells, and intact human blastocysts. Using a cDNA microarray composed of 15,529 cDNAs from known and novel genes, we identify marker transcripts specific to the ICM (e.g., OCT4/POU5F1, NANOG, HMGB1, and DPPA5) and TE (e.g., CDX2, ATP1B3, SFN, and IPL), in addition to novel ICM‐ and TE‐specific expressed sequence tags. The expression patterns suggest that the emergence of pluripotent ICM and TE cell lineages from the morula is controlled by metabolic and signaling pathways, which include inter alia, WNT, mitogen‐activated protein kinase, transforming growth factor‐beta, NOTCH, integrin‐mediated cell adhesion, phosphatidylinositol 3‐kinase, and apoptosis. These data enhance our understanding of the first step in human cellular differentiation and, hence, the derivation of both embryonic stem cells and trophoblastic stem cells from these lineages.
Thyroid dysfunction in pregnancy: definition of TSH cut-off should precede the decision of screening in low-risk pregnant women

Objective. To evaluate the frequency of elevated TSH in pregnant women of low risk for thyroid dysfunction. Subjects and methods. TSH was measured in 838 pregnant women during the first trimester of gestation (from 6 to 14 weeks, median 9 weeks) and who were considered to be of low risk for thyroid dysfunction because they did not meet any of the following criteria: known or clinically suspected thyroid disease; history of head and neck radiotherapy; personal history of autoimmune diseases; family history of thyroid disease; history of abortion or prematurity. Results. The frequency of elevated TSH was 0.25%, 1.2% and 5.5% at cut-off values of 4, 3 and 2.5 mIU/l, respectively. These rates increase to 1.43%, 2.4% and 6.2% if cases of TSH > 2 mIU/l with TPOAb are included. TSH was undetectable in 18 women (2.1%), but only six (0.71%) had elevated T4. Conclusions. The definition of a TSH cut-off that defines subclinical hypothyroidism (SCH) should precede the decision of screening pregnant women without any risk factors for thyroid dysfunction.
Learning a Fuzzy Hyperplane Fat Margin Classifier with Minimum VC dimension

The Vapnik-Chervonenkis (VC) dimension measures the complexity of a learning machine, and a low VC dimension leads to good generalization. The recently proposed Minimal Complexity Machine (MCM) learns a hyperplane classifier by minimizing an exact bound on the VC dimension. This paper extends the MCM classifier to the fuzzy domain. The use of a fuzzy membership is known to reduce the effect of outliers, and to reduce the effect of noise on learning. Experimental results show, that on a number of benchmark datasets, the the fuzzy MCM classifier outperforms SVMs and the conventional MCM in terms of generalization, and that the fuzzy MCM uses fewer support vectors. On several benchmark datasets, the fuzzy MCM classifier yields excellent test set accuracies while using one-tenth the number of support vectors used by SVMs.