Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening wild and semi‐free ranging great apes for putative sexually transmitted diseases: Evidence of Trichomonadidae infections

In Rushmore et al., there was an error that affected the phylogenetic analysis presented in Figure 2. Below is a corrected version of Figure 2, which includes sequences from fecal and urine samples obtained from chimpanzees in our study and other related parasites (with Genbank accession numbers). Full-length (250 ±1 nt) Illumina reads from fecal samples were paired by name and merged using Geneious R9 (Kearse et al., 2012). The resulting 25 unique sequences with TFR-primer sequences were retained. Sequences from urine were acquired using traditional cloning methods from a subset of urine samples (N = 16 samples) instead of Illumina due to trace contaminants among the Illumina reads. We used uclust (Edgar, 2010) implemented in MacQIIME to consolidate sequences with >97% similarity into operational taxonomic units (OTUs) which resulted in three fecal OTUs and five urine OTUs. All sequences were aligned using Geneious alignment with default settings. Phylogenetic reconstruction was performed in Mega7 (Kumar, Stecher, & Tamura, 2016) (Fig. 2). The centroid sequence from each OTU was submitted to Genbank (accession numbers KX017526-KX017533).
Critical Role for CD4+ T Cells in Controlling Retrovirus Replication and Spread in Persistently Infected Mice

ABSTRACT Reactivations of persistent viral infections pose a significant medical problem in immunocompromised cancer, transplant, and AIDS patients, yet little is known about how persistent viral infections are immunologically controlled. Here we describe a mouse model for investigating the role of the immune response in controlling a persistent retroviral infection. We demonstrate that, following recovery from acute Friend virus infection, a small number of B cells evade immunological destruction and harbor persistent virus. In vivo depletions of T-cell subsets in persistently infected mice revealed a critical role for CD4+ T cells in controlling virus replication, spread to the erythroid lineage, and induction of erythroleukemia. The CD4+ T-cell effect was independent of CD8+ T cells and in some cases was also independent of virus-neutralizing antibody responses. Thus, the CD4+ T cells may have had a direct antiviral effect. These results may have relevance for human immunodeficiency virus (HIV) infections where loss of CD4+ T cells is associated with an increase in HIV replication, reactivation of persistent viruses, and a high incidence of virus-associated cancers.
Quantification of MyoD, myogenin, MRF4 and Id-1 by reverse-transcriptase polymerase chain reaction in rat muscles--effects of hypothyroidism and chronic low-frequency stimulation.

A highly sensitive method of reverse-transcriptase polymerase chain reaction (RT-PCR) was established to quantify transcript levels of the myogenic regulatory factors MyoD, myogenin and MRF4 (muscle regulatory factor 4) and for Id-1 (inhibitor of differentiation), a putative negative regulator of myogenesis. The method was sensitive enough to detect mRNA amounts as low as 20 molecules. Measurements in 10 different skeletal muscles of the rat revealed that the amounts of the four factors differ by almost three orders of magnitude. Id-1 is expressed at lowest levels (approximately 4x10(5) molecules/microg RNA) and MRF4 at highest levels (approximately 9x10(7) molecules/microg RNA). In general, myogenin and MyoD mRNAs were inversely distributed in slow and fast muscles. A correlation seemed to exist between the levels of MyoD and myosin heavy chain (MHC) IIb, the fastest MHC isoform. However, as revealed by changes in the expression levels of these two regulatory factors under conditions of hypothyroidism and chronic low-frequency stimulation (CLFS), MyoD and myogenin did not seem to be strictly correlated with fast and slow myosins, respectively. Hypothyroidism led to pronounced depressions of MyoD, but only to small increases in myogenin mRNA in fast muscles. These changes were only slightly increased by CLFS. However, as previously shown, CLFS in combination with hypothyroidism induces in rat muscle pronounced fast to slow transitions in myosin expression [Kirschbaum, B. J., Kucher. H. -B. , Termin, A. , Kelly, A. M. & Pette, D. (1990) J. Biol. Chem. 265, 13974-13980]. These findings suggest that MyoD and myogenin may not be causally related to the development and maintenance of fiber-type diversities.
Profiling microRNA from Brain by Microarray in a Transgenic Mouse Model of Alzheimer's Disease

MicroRNAs (miRNAs) are small noncoding RNAs, which regulate numerous cell functions by targeting mRNA for cleavage or translational repression, and have been found to play an important role in Alzheimer's disease (AD). Our study aimed to identify differentially expressed miRNAs in AD brain as a reference of potential therapeutic miRNAs or biomarkers for this disease. We used amyloid precursor protein (APP) and presenilin 1 (PS1) double transgenic mice and age-matched wild-type (WT) littermates to determine the expression of miRNAs in the brain. MiRNAs were profiled by microarray, and differentially expressed miRNAs underwent target prediction and enrichment analysis. Microarray analysis revealed 56 differentially expressed miRNAs in AD mouse brain, which involved 39 miRNAs that were significantly upregulated and 19 that were downregulated at different ages. Among those miRNAs, a total of 11 miRNAs, including miR-342-3p, miR-342-5p, miR-376c-3p, and miR-301b-3p, were not only conserved in human but also predicted to have targets and signaling pathways closely related to the pathology of AD. In conclusion, in this study, differentially expressed miRNAs were identified in AD brain and proposed as biomarkers, which may have the potential to indicate AD progression. Despite being preliminary, these results may aid in investigating pathological hallmarks and identify effective therapeutic targets.
Effect of Fe/Si ratio in intermetallic compound particles on pitting attacks of 1100 aluminum.

It is well known that elements such as Fe and Si are always contained in an industrial pure aluminum. Some of them dissolve in matrix, others form Al–Fe type or Al–Fe–Si type of the intermetallic compounds. The ratio of Fe/Si in intermetallic compound particles is responsible for the pitting attacks of the aluminum. The degree of the pitting attacks attributes to the preferential dissolution of aluminum and iron in the particles. In this case, the aluminum of the intermetallic compounds is always preferentially dissolved. Then the atmosphere of a particle is changed into low pH by the hydoration of aluminum ions. The higher ratio of Fe/Si is the easier preferential dissolution of iron. The polarization measurements explained that the aluminum and ferrous ions produced by the dissolution make the oxide film around the particle weak and provide a suitable concave for developing the pitting attacks by dissoluting the matrix.
Effect of Maillard reaction on reducing power of malts and beers

Cechovska L. , Konecný M. , Velisek J., Cejpek K. (2012): Effect of Maillard reaction on reducing power of malts and beers. Czech J. Food Sci., 30: 548–556. HPLC with amperometric detection was used to evaluate the reducing power of 23 beers and aqueous extracts of 17 barley malts. While brew pale malts were only slightly higher in electrochemical reducing capacity than natural barleys (about 1.3 g BHAE/kg), caramel malts with the colour of 60–450°EBC showed 7.5–17.2 g BHAE/kg. The superior reducing power of the darker caramel malts was partly due to the presence of a Maillard-derived 2,3-dihydro-3,5dihydroxy-6-methyl-(4h)-pyran-4-one (DDMP), which was responsible for 21–55% of their electrochemical capacity. Among common brew malts, only the Munich type showed a significantly increased electrochemical capacity – 6.8 ± 0.8 g BHAE/kg. In addition to the malts, the brewing can also affect the electrochemical capacity of beers, which ranged from 0.4 ± 0.1 to 1.9 ± 0.3 g BHAE/l. Simple indigenous malt-derived phenolics were responsible for 48–57% of capacity in pale lagers and for 33–45% of it in dark and other specialty lagers. DDMP was not detected in most pale lagers, while it was responsible for up to 11% of the electrochemical capacity in dark and special beers. Highmolecular-weight fraction (> 1kDa) of beers comprised 19–39% (pale lagers) and 14–21% (dark and special beers) of the capacity. The reducing power of malts and beers determined by the amperometric method was confirmed by a good correlation with the results of DPPH• scavenging assay.
Induction of Interferon-Stimulated Genes on the IL-4 Response Axis by Epstein-Barr Virus Infected Human B Cells; Relevance to Cellular Transformation

Epstein-Barr virus (EBV) is an oncogenic virus that is associated with the pathogenesis of several human lymphoid malignancies, including Hodgkin's lymphoma. Infection of normal resting B cells with EBV results in activation to lymphoblasts that are phenotypically similar to those generated by physiological stimulation with CD40L plus IL-4. One important difference is that infection leads to the establishment of permanently growing lymphoblastoid cell lines, whereas CD40L/IL-4 blasts have finite proliferation lifespans. To identify early events which might later determine why EBV infected blasts go on to establish transformed cell lines, we performed global transcriptome analyses on resting B cells and on EBV and CD40L/IL-4 blasts after 7 days culture. As anticipated there was considerable overlap in the transcriptomes of the two types of lymphoblasts when compared to the original resting B cells, reflecting common changes associated with lymphocyte activation and proliferation. Of interest to us was a subset of 255 genes that were differentially expressed between EBV and CD40L/IL-4 blasts. Genes which were more highly expressed in EBV blasts were substantially and significantly enriched for a set of interferon-stimulated genes which on further in silico analyses were found to be repressed by IL-4 in other cell contexts and to be up-regulated in micro-dissected malignant cells from Hodgkin's lymphoma biopsies when compared to their normal germinal center cell counterparts. We hypothesized that EBV and IL-4 were targeting and discordantly regulating a common set of genes. This was supported experimentally in our B cell model where IL-4 stimulation partially reversed transcriptional changes which follow EBV infection and it impaired the efficiency of EBV-induced B cell transformation. Taken together, these data suggest that the discordant regulation of interferon and IL-4 pathway genes by EBV that occurs early following infection of B cells has relevance to the development or maintenance of an EBV-associated malignancy.
Clinical Features and Treatment Modes of Mandibular Fracture at the Department of Oral and Maxillofacial Surgery, Shimane University Hospital, Japan

Background The number of elderly patients with maxillofacial trauma is rapidly increasing due to active lifestyles and longevity. Shimane prefecture has the fastest growing proportion of elderly individuals in Japan. The aim of this study was to reveal the distinctive features and treatment modes of mandibular fracture treatment mode in patients requiring hospitalization at the Department of Oral and Maxillofacial Surgery, Shimane University Hospital, Japan. Patients and Methods Patient age, sex, period between injury and first consultation, years since injury, cause of injury, fracture site, treatment, and duration of hospitalization were evaluated. Univariate Poisson regression, relative risk with 95% confidence interval based on the Wald test, Fisher’s exact test, and Kruskal-Wallis test were used to explore associations among clinical and demographic variables. Results In total, 305 patients were diagnosed with and hospitalized for mandibular fracture from 1980 to 2010. Younger age increased the risk for mandibular fracture. Incidence was higher in males than females, particularly in the young, but the male to female ratio decreased with age. The period until first hospital consultation decreased progressively over the study period. Fall was a much more frequent cause in patients aged ≥60 than in those aged <60 years. Mandibular fracture with condyle, symphysis, and angle involvement were most common and were associated with sex, age, and treatment mode. Length of hospitalization has decreased since 1980. Conclusion In our department, patients aged ≥60 years accounted for a greater proportion of mandibular fracture cases than in many previous studies, reflecting the greater proportion of elderly residents in Shimane prefecture.
Limitations of using same-hospital readmission metrics.

OBJECTIVE To quantify the limitations associated with restricting readmission metrics to same-hospital only readmission. DESIGN Using 2000-2009 California Office of Statewide Health Planning and Development Patient Discharge Data Nonpublic file, we identified the proportion of 7-, 15- and 30-day readmissions occurring to the same hospital as the initial admission using All-cause Readmission (ACR) and 3M Corporation Potentially Preventable Readmissions (PPR) Metric. We examined the correlation between performance using same and different hospital readmission, the percent of hospitals remaining in the extreme deciles when utilizing different metrics, agreement in identifying outliers and differences in longitudinal performance. Using logistic regression, we examined the factors associated with admission to the same hospital. RESULTS 68% of 30-day ACR and 70% of 30-day PPR occurred to the same hospital. Abdominopelvic procedures had higher proportions of same-hospital readmissions (87.4-88.9%), cardiac surgery had lower (72.5-74.9%) and medical DRGs were lower than surgical DRGs (67.1 vs. 71.1%). Correlation and agreement in identifying high- and low-performing hospitals was weak to moderate, except for 7-day metrics where agreement was stronger (r = 0.23-0.80, Kappa = 0.38-0.76). Agreement for within-hospital significant (P < 0.05) longitudinal change was weak (Kappa = 0.05-0.11). Beyond all patient refined-diagnostic related groups, payer was the most predictive factor with Medicare and MediCal patients having a higher likelihood of same-hospital readmission (OR 1.62, 1.73). CONCLUSIONS Same-hospital readmission metrics are limited for all tested applications. Caution should be used when conducting research, quality improvement or comparative applications that do not account for readmissions to other hospitals.
Measurements and evaluation of regional innovation capacity and spatial difference

This study aims to improve measurement of regional innovation capacity and assess regional innovation capacity of 31 provinces and cities in China. Use of factor analysis provided an empirical validation of measurement of 33 indicators of regional innovation capacity. Three factors were extracted and named as innovation input, innovation out and innovation environment. The result was a set of measurements index that could be used to assess resources and performance of regional innovation capacity on key dimensions, which could result in more efficient and more effective public policy set by government. In the end, innovative capacity of 31 provinces and cities in China were evaluated and compared, we found there were the significant spatial difference among them.
Predictors and prognostic importance of weight change in adult solid tumors.

103 Background: Body weight change in adults with solid tumors was examined in outpatients. Objective was to determine if demographics, clinical and biochemical characteristics were associated with change in weight between visit 1 and visit 2. Examine if weight change and related parameters were associated with survival. METHODS Electronic medical records (EMR) from a tertiary cancer center retrospectively reviewed from 2009-2011. Body weight and other clinical parameters on visit 1 - within a year post diagnosis; visit 2 ≥3 weeks after visit 1. Weight change categorized as: weight gain, 0-5%, 5.01-10%, >10%. Ordinal logistic regression and Cox proportional hazards utilized for WL predictors and prognostic factors respectively. RESULTS N = 5,901; Mean age (±SD): 61 ± 12 years; 82% were Caucasians; 16% African Americans. Common cancers were prostate 19%; breast 15%; lung 15%; head and neck 6%; colorectal 6%; others 12%. Metastatic disease was present in 18%. Bone, brain, lymph nodes - were common metastatic sites. 45% had radiotherapy; 41% chemotherapy. Median weight change from visit 1 to visit 2 = -1 (-48, 66) kgs. Weight loss (WL) in 57% (≤5%: 30%, 5.01-10%: 13%, >10%: 14%). Different primary cancer sites, number of metastatic sites, radiotherapy/chemotherapy/hormonal therapies, older age, body mass index (BMI), and albumin predicted weight change. Median survival in 5.01-10.0% WL= 9.4 months, >10.0% = 5.3 months, and not observed ≤ 5%. CONCLUSIONS 1. Majority lost ≤5% of body weight by visit 2. 2. Esophagus, head and neck, and pancreas (primary) - the greatest risk of WL; prostate - lowest. 3. High BMI predicted greater WL compared to normal or underweight. 4. ≤5% WL had a survival advantage compared to 5.01-10% and >10%. 5. WL remained prognostic for survival after adjusting for other prognostic factors.
Intuitive Choices Lead to Intensified Positive Emotions: An Overlooked Reason for “Intuition Bias”?

People have, for many well-documented reasons, a tendency to overemphasize their intuitions and to follow them, even when they should not. This “intuition bias” leads to several kinds of specific intuitive biases in judgments and decision making. Previous studies have shown that characteristics of the decision process have a tendency to “leak” into the experience of the choice outcome. We explore whether intuitive choices influence the experience of the choice outcomes differently from “non-intuitive,” analytic choices. Since intuition is feeling based, we examine in particular if intuitive choices have stronger affective consequences than non-intuitive ones. Participants in two scenario studies (N = 90; N = 126) rated the feelings of decision makers who experienced a conflict between two options, one intuitively appealing and another that appeared preferable on analytic grounds. Choosing the intuitive alternative was anticipated to lead to somewhat more regret after negative outcomes and, in particular, much more satisfaction with positive outcomes. In two autobiographical studies, one with psychology students (N = 88) and the other with experienced engineers (N = 99), participants were asked to provide examples of choice conflicts between an intuitive and a non-intuitive option from their own private or professional lives. Both groups showed a tendency to report stronger emotions, in particular positive, after intuitive choices. One well-established explanation for intuition bias focuses on the nature of people’s anticipated negative counterfactual thoughts if their decisions were to turn out badly. The present data indicate that intuitive choices intensify positive emotions, anticipated and real, after successful outcomes much more than negative emotions after failures. Positive outcomes are also more commonly expected than negative ones, when we make choices. We argue that markedly amplified emotions, mediated by stronger personal involvement, in the positive outcomes of intuitive versus non-intuitive choices, is an overlooked reason for intuition bias.
Trapping and Propelling Microparticles at Long Range by Using an Entirely Stripped and Slightly Tapered No-Core Optical Fiber

A stripped no-core optical fiber with a 125 μm diameter was transformed into a symmetric and unbroken optical fiber that tapers slightly to a 45-μm-diameter waist. The laser light can be easily launched into the no-core optical fiber. The enhanced evanescent wave of the slightly tapered no-core optical fiber can attract nearby 5-μm-diameter polystyrene microparticles onto the surface of the tapered multimode optical fiber within fast flowing fluid and propel the trapped particles in the direction of the light propagation to longer delivery range than is possible using a slightly tapered telecom single-mode optical fiber.
What does preexposure prophylaxis mean for treatment; what does treatment mean for preexposure prophylaxis?

Purpose of reviewBoth preexposure prophylaxis (PrEP) and treatment as prevention (TaP) have shown promise in contributing to HIV prevention, in models, observational cohorts and in real-world intervention studies. They share similarities, in that they use the same drugs, toxicity markers and may be focused on the same key populations. How to implement PrEP is still the source of much debate; effective coverage with TaP, with recent data on the positive impact of treatment at high CD4 counts, is still an ongoing challenge. Recent findingsTreatment has demonstrated individual benefit even at CD4 counts above 350 cells/&mgr;l; PrEP has shown the effectiveness in real-world use. SummaryThis article discusses the intersection of the two interventions, some programmatic misconceptions and complexities, and argues that PrEP is a nuanced and useful adjunct to HIV programmes. PrEP can be rolled out in a way that complements treatment, possibly even within primary health clinics, and may be required for the many people in whom TaP currently fails. PrEP will need constant adaptation so as to maintain programmatic and cost–effectiveness, as the epidemiology of HIV changes with TaP rollout and expansion as CD4 restrictions are lifted. Finally, the article also argues that so-called ethical concerns around competing resources are relatively easily resolved.
The Exposed Proteomes of Brachyspira hyodysenteriae and B. pilosicoli

Brachyspira hyodysenteriae and Brachyspira pilosicoli are well-known intestinal pathogens in pigs. B. hyodysenteriae is the causative agent of swine dysentery, a disease with an important impact on pig production while B. pilosicoli is responsible of a milder diarrheal disease in these animals, porcine intestinal spirochetosis. Recent sequencing projects have provided information for the genome of these species facilitating the search of vaccine candidates using reverse vaccinology approaches. However, practically no experimental evidence exists of the actual gene products being expressed and of those proteins exposed on the cell surface or released to the cell media. Using a cell-shaving strategy and a shotgun proteomic approach we carried out a large-scale characterization of the exposed proteins on the bacterial surface in these species as well as of peptides and proteins in the extracellular medium. The study included three strains of B. hyodysenteriae and two strains of B. pilosicoli and involved 148 LC-MS/MS runs on a high resolution Orbitrap instrument. Overall, we provided evidence for more than 29,000 different peptides pointing to 1625 and 1338 different proteins in B. hyodysenteriae and B. pilosicoli, respectively. Many of the most abundant proteins detected corresponded to described virulence factors and vaccine candidates. The level of expression of these proteins, however, was different among species and strains, stressing the value of determining actual gene product levels as a complement of genomic-based approaches for vaccine design.