Miracle-dz/UniFAR-FTUs huggingface dataset:
Univariate Analysis to Examine Predictors of Response to Leukocytapheresis in Ulcerative Colitis Patients

Leukocytapheresis (LCAP) is reportedly effective for the treatment of active ulcerative colitis (UC) and is a therapeutic option for steroid‐dependent or steroid‐resistant patients with UC. However, a consensus regarding the use of LCAP for UC patients has not yet been established. Therefore, we analyzed patients' records to identify predictors of response to LCAP therapy and subsequent recurrence. Between October 2001 and March 2011, we recruited 41 patients who had been diagnosed as having UC and had received LCAP therapy. Patients diagnosed with moderate to severe UC with left‐side or total colitis and received LCAP therapy for the first time were enrolled. We retrospectively performed a univariate analysis using the patients' medical records to identify factors affecting the therapeutic effect of LCAP. Body mass index exceeding 18.5 kg/m2 was found to influence the therapeutic effect of LCAP. Male sex was correlated with a rapid response to LCAP treatment and the maintenance of remission. UC patients experiencing their first attack or had an elevated C‐reactive protein level prior to LCAP therapy exhibited a relatively long remission period. In the “after LCAP therapy” group, a low Rachmilewitz endoscopic score, low erythrocyte sedimentation rate, or high white blood cell count was associated with a long remission period. Our results suggest that LCAP should be performed for the treatment of early‐onset UC. LCAP can be expected to induce a long remission period, enabling mucosal healing, although the factors that affected the remission period did not influence the therapeutic effect and responsiveness.
Automatic Evaluation of Chinese Translation Output: Word-Level or Character-Level?

Word is usually adopted as the smallest unit in most tasks of Chinese language processing. However, for automatic evaluation of the quality of Chinese translation output when translating from other languages, either a word-level approach or a character-level approach is possible. So far, there has been no detailed study to compare the correlations of these two approaches with human assessment. In this paper, we compare word-level metrics with character-level metrics on the submitted output of English-to-Chinese translation systems in the IWSLT'08 CT-EC and NIST'08 EC tasks. Our experimental results reveal that character-level metrics correlate with human assessment better than word-level metrics. Our analysis suggests several key reasons behind this finding.
Ammonia threshold for inhibition of anaerobic digestion of thin stillage and the importance of organic loading rate

Biogas production from nitrogen‐rich feedstock results in release of ammonia (NH3), causing inhibition of the microbial process. The reported threshold ammonia value for stable biogas production varies greatly between studies, probably because of differences in operating conditions. Moreover, it is often difficult to separate the effect of ammonia inhibition from that of organic loading rate (OLR), as these two factors are often interrelated. This study attempted to distinguish the effects of ammonia and OLR by analysis of two laboratory‐scale biogas reactors operating with thin stillage and subjected to an increase in free ammonia (from 0.30 to 1.1 g L−1) either by addition of an external nitrogen source (urea) or by increasing the OLR (3.2–6.0 g volatile solids L−1 d−1). The results showed that ammonia concentration was detrimental for process performance, with the threshold for stability in both processes identified as being about 1 g NH3‐N L−1, irrespective of OLR. Analysis of the methanogenic community showed limited differences between the two reactors on order level and a clear increase in the abundance of Methanomicrobiales, particularly Methanoculleus sp. , in response to increasing ammonia concentration. Further comprehensive molecular analysis revealed that diverse Methanoculleus species dominated in the reactors at a given ammonia level at different OLR. The acetogenic community was clearly affected by both ammonia concentration and OLR, suggesting that the volatile fatty acid load in relation to the higher OLR was important for the dynamics of this community.
Coordinated regulation of the ESCRT-III component CHMP4C by the chromosomal passenger complex and centralspindlin during cytokinesis

The chromosomal passenger complex (CPC)—composed of Aurora B kinase, Borealin, Survivin and INCENP—surveys the fidelity of genome segregation throughout cell division. The CPC has been proposed to prevent polyploidy by controlling the final separation (known as abscission) of the two daughter cells via regulation of the ESCRT-III CHMP4C component. The molecular details are, however, still unclear. Using atomic force microscopy, we show that CHMP4C binds to and remodels membranes in vitro. Borealin prevents the association of CHMP4C with membranes, whereas Aurora B interferes with CHMP4C's membrane remodelling activity. Moreover, we show that CHMP4C phosphorylation is not required for its assembly into spiral filaments at the abscission site and that two distinctly localized pools of phosphorylated CHMP4C exist during cytokinesis. We also characterized the CHMP4C interactome in telophase cells and show that the centralspindlin complex associates preferentially with unphosphorylated CHMP4C in cytokinesis. Our findings indicate that gradual dephosphorylation of CHMP4C triggers a ‘relay’ mechanism between the CPC and centralspindlin that regulates the timely distribution and activation of CHMP4C for the execution of abscission.
Translation efficiency is determined by both codon bias and folding energy

Synonymous mutations do not alter the protein produced yet can have a significant effect on protein levels. The mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at the beginning of genes is the dominant factor via its effect on translation initiation. Using the Escherichia coli and Saccharomyces cerevisiae transcriptomes, we conducted a genome-scale study aiming at dissecting the determinants of translation efficiency. There is a significant association between codon bias and translation efficiency across all endogenous genes in E. coli and S. cerevisiae but no association between folding energy and translation efficiency, demonstrating the role of codon bias as an important determinant of translation efficiency. However, folding energy does modulate the strength of association between codon bias and translation efficiency, which is maximized at very weak mRNA folding (i.e., high folding energy) levels. We find a strong correlation between the genomic profiles of ribosomal density and genomic profiles of folding energy across mRNA, suggesting that lower folding energies slow down the ribosomes and decrease translation efficiency. Accordingly, we find that selection forces act near uniformly to decrease the folding energy at the beginning of genes. In summary, these findings testify that in endogenous genes, folding energy affects translation efficiency in a global manner that is not related to the expression levels of individual genes, and thus cannot be detected by correlation with their expression levels.
Does Delay Cause Decay? The Effect of Administrative Decision Time on the Labor Force Participation and Earnings of Disability Applicants

An influential body of research studies the labor supply and earnings of denied Social Security Disability Insurance (SSDI) applicants to estimate the potential employment and earnings of those awarded benefits. This research design implicitly treats employability as a stable applicant attribute that is not directly impacted by the process of applying for SSDI benefits. If, plausibly, applicants’ employment potential deteriorates while they are out of the labor force, then the labor force participation of denied applicants -- who spend an average of 10 months seeking benefits -- may understate their employment potential at the time of application. This paper tests whether the duration of SSDI applications causally affects applicants’ subsequent employment. We use a unique Social Security Administration workload database to identify exogenous variation in applicants’ initial decision times induced by differences in processing speed among the disability examiners to which they are randomly assigned. This variation significantly affects applicants’ total processing time but, importantly, is uncorrelated with their initial award and denial outcomes. We find that longer processing times reduce the employment and earnings of SSDI applicants in the years after their initial decision. A one standard deviation (2.4 month) increase in initial processing time reduces annual employment rates by 1 percentage point (3.2%) in years two, three and four post-decision. Extrapolating these effects to total applicant processing times, we estimate that the SSDI determination process directly reduces the post-application employment of denied applicants by approximately 3.6 percentage points (7%) and allowed applicants by approximately 5.2 percentage points (33%).
MiR-7 Triggers Cell Cycle Arrest at the G1/S Transition by Targeting Multiple Genes Including Skp2 and Psme3

MiR-7 acts as a tumour suppressor in many cancers and abrogates proliferation of CHO cells in culture. In this study we demonstrate that miR-7 targets key regulators of the G1 to S phase transition, including Skp2 and Psme3, to promote increased levels of p27KIP and temporary growth arrest of CHO cells in the G1 phase. Simultaneously, the down-regulation of DNA repair-specific proteins via miR-7 including Rad54L, and pro-apoptotic regulators such as p53, combined with the up-regulation of anti-apoptotic factors like p-Akt, promoted cell survival while arrested in G1. Thus miR-7 can co-ordinate the levels of multiple genes and proteins to influence G1 to S phase transition and the apoptotic response in order to maintain cellular homeostasis. This work provides further mechanistic insight into the role of miR-7 as a regulator of cell growth in times of cellular stress.
TLR 5 Signaling Enhances the Proliferation of Human Allogeneic CD 40-Activated B Cell Induced CD 4 hiCD 25 + Regulatory T Cells

Although diverse functions of different toll-like receptors (TLR) on human natural regulatory T cells have been demonstrated recently, the role of TLR-related signals on human induced regulatory T cells remain elusive. Previously our group developed an ex vivo high-efficient system in generating human alloantigen-specific CD4CD25 regulatory T cells from naı̈ve CD4CD25 T cells using allogeneic CD40-activated B cells as stimulators. In this study, we investigated the role of TLR5related signals on the generation and function of these novel CD4CD25 regulatory T cells. It was found that induced CD4CD25 regulatory T cells expressed an up-regulated level of TLR5 compared to their precursors. The blockade of TLR5 using anti-TLR5 antibodies during the co-culture decreased CD4CD25 regulatory T cells proliferation by induction of S phase arrest. The S phase arrest was associated with reduced ERK1/2 phosphorylation. However, TLR5 blockade did not decrease the CTLA-4, GITR and FOXP3 expressions, and the suppressive function of CD4CD25 regulatory T cells. In conclusion, we discovered a novel function of TLR5-related signaling in enhancing the proliferation of CD4CD25 regulatory T cells by promoting S phase progress but not involved in the suppressive function of human CD40-activated B cell-induced CD4CD25 regulatory T cells, suggesting a novel role of TLR5-related signals in the generation of induced regulatory T cells. Citation: Chan P-L, Zheng J, Liu Y, Lam K-T, Xiang Z, et al. (2013) TLR5 Signaling Enhances the Proliferation of Human Allogeneic CD40-Activated B Cell Induced CD4CD25 Regulatory T Cells. PLoS ONE 8(7): e67969. doi:10.1371/journal.pone. 0067969 Editor: Kin Mang Lau, The Chinese University of Hong Kong, Hong Kong Received April 15, 2013; Accepted May 23, 2013; Published July 3, 2013 Copyright: 2013 Chan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported in part by NSFC/RGC Joint Research Scheme (N_HKU 747/11), General Research Fund, Research Grants Council of Hong Kong (HKU 781211M); Area of Excellence program (AoE/M-12/06), University Grants Committee of Hong Kong Special Administrative Region. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: wwtu@hku.hk
Immunological and Molecular Characterization of Susceptibility in Relationship to Bacterial Strain Differences in Mycobacterium avium subsp. paratuberculosis Infection in the Red Deer (Cervus elaphus)

ABSTRACT Johne's disease (JD) infection, caused by Mycobacterium avium subsp. paratuberculosis, represents a major disease problem in farmed ruminants. Although JD has been well characterized in cattle and sheep, little is known of the infection dynamics or immunological response in deer. In this study, typing of M. avium subsp. paratuberculosis isolates from intestinal lymphatic tissues from 74 JD-infected animals showed that clinical isolates of M. avium subsp. paratuberculosis from New Zealand farmed red deer were exclusively of the bovine strain genotype. The susceptibility of deer to M. avium subsp. paratuberculosis was further investigated by experimental oral-route infection studies using defined isolates of virulent bovine and ovine M. avium subsp. paratuberculosis strains. Oral inoculation with high (109 CFU/animal) or medium (107 CFU/animal) doses of the bovine strain of M. avium subsp. paratuberculosis established 100% infection rates, compared to 69% infection following inoculation with a medium dose of the ovine strain. The high susceptibility of deer to the bovine strain of M. avium subsp. paratuberculosis was confirmed by a 50% infection rate following experimental inoculation with a low dose of bacteria (103 CFU/animal). This study is the first to report experimental M. avium subsp. paratuberculosis infection in red deer, and it outlines the strong infectivity of bovine-strain M. avium subsp. paratuberculosis isolates for cervines.
Validity of self-reported hysterectomy: a prospective cohort study within the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS)

Objective To evaluate the validity of self-reported hysterectomy against the gold standard of uterine visualisation using pelvic ultrasound. Design Prospective cohort study. Setting UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) based in 13 National Health Service (NHS) Trusts in England, Wales and Northern Ireland. Participants Between April 2001 and October 2005, 48 215 postmenopausal women aged 50–74 randomised to the ultrasound screening arm of UKCTOCS underwent the first (initial) scan on the trial. Interventions At recruitment, the women completed a recruitment questionnaire (RQ) which included previous hysterectomy. The sonographer asked each woman regarding previous hysterectomy (interview format, IF) prior to the scan. At the scan, in addition to ovarian morphology, endometrial thickness (ET)/endometrial abnormality were captured if the uterus was visualised at the scan. Outcome measures Self-reported hysterectomy at RQ or IF was compared to ultrasound data on ET/endometrial abnormality (as surrogate uterine visualisation markers) on the first (initial) scan. Results Of 48 215 women, 3 had congenital uterine agenesis and 218 inconclusive results. The uterus was visualised in 39 121 women. 8871 self-reported hysterectomy at RQ, 8641 at IF and 8487 at both. The uterus was visualised in 39 123, 39 353 and 38 969 women not self-reporting hysterectomy at RQ, IF or both. Validity, sensitivity, specificity, positive predictive value and negative predictive value of using RQ alone, IF or both RQ/IF were 99.6%, 98.9%, 99.7%, 98.9% and 99.7%; 98.9%, 98.4%, 99.1%, 95.9% and 99.7%; 99.8%, 99.6%, 99.9%, 99.4% and 99.9%, respectively. Conclusions Self-reported hysterectomy is a highly accurate and valid source for studying long-term associations of hysterectomy with disease onset. Trial registration International Standard Randomised Controlled Trial Number (ISRCTN)—22488978
The Deuterium-to-Hydrogen Ratio in a Low-Metallicity Cloud Falling onto the Milky Way

Using Far Ultraviolet Spectroscopic Explorer (FUSE) and Hubble Space Telescope observations of the QSO PG 1259+593, we detect D I Lyman series absorption in high-velocity cloud Complex C, a low-metallicity gas cloud falling onto the Milky Way. This is the first detection of atomic deuterium in the local universe in a location other than the nearby regions of the Galactic disk. We construct a velocity model for the sight line based on the numerous O I absorption lines detected in the ultraviolet spectra. We identify eight absorption-line components, two of which are associated with the high-velocity gas in Complex C at ≈-128 and ≈-112 km s-1. A new Westerbork Synthesis Radio Telescope (WSRT) interferometer map of the H I 21 cm emission toward PG 1259+593 indicates that the sight line passes through a compact concentration of neutral gas in Complex C. We use the WSRT data together with single-dish data from the Effelsberg 100 m radio telescope to estimate the H I column density of the high-velocity gas and to constrain the velocity extents of the H I Lyman series absorption components observed by FUSE. We find N(H I) = (9.0 ± 1.0) × 1019 cm-2, N(D I) = (2.0 ± 0.6) × 1015 cm-2, and N(O I) = (7.2 ± 2.1) × 1015 cm-2 for the Complex C gas (68% confidence intervals). The corresponding light-element abundance ratios are D/H = (2.2 ± 0.7) × 10-5, O/H = (8.0 ± 2.5) × 10-5, and D/O = 0.28 ± 0.12. The metallicity of Complex C gas toward PG 1259+593 is approximately 1/6 solar, as inferred from the oxygen abundance [O/H] = -0.79 ±. While we cannot rule out a value of D/H similar to that found for the local ISM (i.e., D/H ∼ 1.5 × 10-5), we can confidently exclude values as low as those determined recently for extended sight lines in the Galactic disk (D/H < 1 × 10-5). Combined with the sub-solar metallicity estimate and the low nitrogen abundance, this conclusion lends support to the hypothesis that Complex C is located outside the Milky Way, rather than inside in material recirculated between the Galactic disk and halo. The value of D/H for Complex C is consistent with the primordial abundance of deuterium inferred from recent Wilkinson Microwave Anisotropy Probe observations of the cosmic microwave background and simple chemical evolution models that predict the amount of deuterium astration as a function of metallicity.
Recovery of Activities of Daily Living Among Older People One Year After Hip Fracture

This article aims to determine the functional recovery of older people, who were previously independent in activities of daily living (ADLs) and without cognitive impairment, in the year following a fall-related hip fracture. A cohort study was carried out among patients admitted to University General Hospital of Albacete (Spain). Consecutive sampling was performed. Variables included demographic, habitual residence, type of hip fracture, mental status (Short Portable Mental Status Questionnaire [SPMSQ] Pfeiffer), and independence in ADLs (according to the Barthel Index [BI]) prior to the fall and after the fracture. For 205 patients, 1 year after surgery, the mean BI score was 78.09 (SD = 25.13); (vs. 90.02 before the hip fracture), 59% showed urinary continence (vs. 79%), and 65% walked without assistance (vs. 82%). Regarding predictors of recovery, results indicate that patients who are older, who suffer complications after hospital discharge, or who reside in nursing homes experience poorer recovery in ADLs. Only 47.9% of the patients regained prior levels of autonomy 1 year after surgery.
Bt-toxin uptake by the non-target herbivore, Myzus persicae (Hemiptera: Aphididae), feeding on transgenic oilseed rape in laboratory conditions

Abstract The potential non-target effects of genetically modified crops are some of the more debated topics within applied biotechnologies in agriculture and environmental risk assessment. The objective of the present research was to study the potential Bt-toxin uptake by the non-target herbivore Myzus persicae Sulzer (Hemiptera: Aphididae) feeding on transgenic oilseed rape plants (Brassica napus cv. ‘Westar’ lines GT 2–4) expressing the Cry1Ac endotoxin. A specific aim was to replicate our previous experiment in controlled laboratory conditions to avoid or minimize the risk of contamination leading to potential false positive results. The toxin levels in vernalized (V) and not-vernalized (not-V) transgenic oilseed rape plants was also monitored to better clarify the role of physiological processes on Bt-toxin expression. Cry1Ac expression in not-V plants (mean concentration±SE=167.8±5.7 μg kg−1 FW) showed a pattern of large variability, in comparison with V plants whose expression (mean concentration±SE=227.7±1.9 μg kg−1 FW) was significantly more stable. Cry1Ac toxin was detected in three aphid samples reared on V plants with a mean toxin concentration±SE of 4.8±0.6 μg Kg−1 FW and in three out of six samples of aphids reared on not-V plants (mean toxin concentration±SE=7.1±1.2 μg kg−1 FW). The mean Bt-toxin concentration of all the positive aphid samples was 5.9±1.0 μg kg−1 FW. Our results confirmed the findings of our previous experiment and highlighted the potential for Cry1Ac toxin uptake by aphids feeding on transgenic oilseed rape plants.
Correlation of the Virological Response to Short-Term Maraviroc Monotherapy with Standard and Deep-Sequencing-Based Genotypic Tropism Prediction Methods

ABSTRACT Genotypic tropism testing methods are emerging as the first step before prescription of the CCR5 antagonist maraviroc (MVC) to HIV-infected patients in Europe. Studies validating genotypic tests have included other active drugs that could have potentially convoluted the effects of MVC. The maraviroc clinical test (MCT) is an in vivo drug sensitivity test based on the virological response to a short-term exposure to MVC monotherapy. Thus, our aim was to compare the results of genotypic tropism testing methods with the short-term virological response to MVC monotherapy. A virological response in the MCT was defined as a ≥1-log10 decrease in HIV RNA or undetectability after 8 days of drug exposure. Seventy-three patients undergoing the MCT were included in this study. We used both standard genotypic methods (n = 73) and deep sequencing (n = 27) on MCT samples at baseline. For the standard methods, the most widely used genotypic algorithms for analyzing the V3 loop sequence, geno2pheno and PSSM, were used. For deep sequencing, the geno2pheno algorithm was used with a false-positive rate cutoff of 3.5. The discordance rates between the standard genotypic methods and the virological response were approximately 20% (including mostly patients without a virological response). Interestingly, these discordance rates were similar to that obtained from deep sequencing (18.5%). The discordance rates between the genotypic methods (tropism assays predictive of the use of the CCR5 coreceptor) and the MCT (in vivo MVC sensitivity assay) indicate that the algorithms used by genotypic methods are still not sufficiently optimized.