Miracle-dz/UniFAR-FTUs huggingface dataset:
Xenotropic Mouse Gammaretroviruses Isolated from Pre-Leukemic Tissues Include a Recombinant

Naturally-occurring lymphomagenesis is induced by mouse leukemia viruses (MLVs) carried as endogenous retroviruses (ERVs). Replicating the ecotropic MLVs recombines with polytropic (P-ERVs) and xenotropic ERVs (X-ERVs) to generate pathogenic viruses with an altered host range. While most recovered nonecotropic recombinants have a polytropic host range, the X-MLVs are also present in the pre-leukemic tissues. We analyzed two such isolates from the AKR mice to identify their ERV progenitors and to look for evidence of recombination. AKR40 resembles the active X-ERV Bxv1, while AKR6 has a Bxv1-like backbone with substitutions that alter the long terminal repeat (LTR) enhancer and the envelope (env). AKR6 has a modified xenotropic host range, and its Env residue changes all lie outside of the domain that governs the receptor choice. The AKR6 segment spanning the two substitutions, but not the entire AKR6 env-LTR, exists as an ERV, termed Xmv67, in AKR, but not in the C57BL/6 mice. This suggests that AKR6 is the product of one, not two, recombination events. Xmv67 originated in the Asian mice. These data indicate that the recombinant X-MLVs that can be generated during lymphomagenesis, describe a novel X-ERV subtype found in the AKR genome, but not in the C57BL/6 reference genome, and identify residues in the envelope C-terminus that may influence the host range.
Supporting Historical Research Through User-Centered Visual Analytics

In this paper we describe the development and evaluation of a visual analytics tool to support historical research. Historians continuously gather data related to their scholarly research from archival visits and background search. Organising and making sense of all this data can be challenging as many historians continue to rely on analog or basic digital tools. We built an integrated note-taking environment for historians which unifies a set of func-tionalities we identified as important for historical research including editing, tagging, searching, sharing and visualization. Our approach was to involve users from the initial stage of brainstorming and requirement analysis through to design, implementation and evaluation. We report on the process and results of our work, and conclude by reflecting on our own experience in conducting user-centered visual analytics design for digital humanities.
Individualized Immunological Data for Precise Classification of OCD Patients

Obsessive–compulsive disorder (OCD) affects about 2% of the general population, for which several etiological factors were identified. Important among these is immunological dysfunction. This review aims to show how immunology can inform specific etiological factors, and how distinguishing between these etiologies is important from a personalized treatment perspective. We found discrepancies concerning cytokines, raising the hypothesis of specific immunological etiological factors. Antibody studies support the existence of a potential autoimmune etiological factor. Infections may also provoke OCD symptoms, and therefore, could be considered as specific etiological factors with specific immunological impairments. Finally, we underline the importance of distinguishing between different etiological factors since some specific treatments already exist in the context of immunological factors for the improvement of classic treatments.
Ambient Air Currents Activate Corneal Nerves During Ocular Desiccation in Rats: Simultaneous Recordings of Neural Activity and Corneal Temperature

Purpose Previously we found two types of corneal neurons that we hypothesized to play an important role in tearing. One type is called low threshold–cold sensitive plus dry sensitive (LT-CS + DS), and the other is termed high threshold–cold sensitive plus dry sensitive (HT-CS + DS). The present study examined critical stimuli influencing the activity of these neurons to elucidate environmental factors that may trigger this ocular reflex. Methods Single corneal neurons were extracellularly recorded from the trigeminal ganglia in response to ocular stimuli that mimic environmental conditions one encounters in daily life. They included an ocular desiccation and slight air currents and were presented while simultaneously monitoring the ocular surface temperatures (OST) in rats. Results The results showed that the changes in steady state (SS) activity of the neurons closely followed the changes in SS OST: during the sustained ocular desiccation, neural firing displayed numerous small sudden increases in activities (“spiking”); these “spiking” activities of LT-CS + DS neurons were replicated by a minute air current that induced slight ocular surface cooling of approximately 0.2–0.1°C; and the responses of HT-CS + DS neurons showed an inconsistent relationship to the changes in SS OST or exhibited little evidence for “spiking” activities. Conclusions These results suggest that LT-CS + DS neurons play a role in the afferent trigger of tearing as we face the environment, exposing the cornea to prevailing air currents that produce a slight cooling of the ocular surface. By contrast, HT-CS + DS neurons may serve to protect the eyes from extreme dryness by eliciting nociception-evoked tearing when the OST or osmolarity of tears becomes injurious.
3D Simulations of Ultra-small MOSFETs with Real-space Treatment of the Electron - Electron and Electron-ion Interactions

We present a 3D Ensemble Monte Carlo particle-based simulator with a novel realspace treatment of the short-range electron – electron and electron-ion interactions. By using a corrected Coulomb force in conjunction with a proper cutoff range, the shortrange portion of the force is properly accounted for, and the ‘double counting’ of the long-range interaction is eliminated. The proposed method naturally incorporates the multi-ion contributions, local distortions in the scattering potential due to the movement of the free charges, and carrier-density fluctuations. The doping dependence of the low-field mobility obtained from 3D resistor simulations closely follows experimental results, thus supporting the appropriateness of the proposed scheme. Simulations of ultra-small MOSFETs demonstrate that the short-range electron – electron and electronion interactions are responsible for the fast thermalization of the carriers at the drain end of the device, which occurs over distances that are on the order of few nanometers. The omission of the short-range portions of these two interaction terms leads to significant overestimation of the distance over which carriers thermalize.
Using a Virtual Lidar Approach to Assess the Accuracy of the Volumetric Reconstruction of a Wind Turbine Wake

Scanning Doppler lidars are the best tools for acquiring 3D velocity fields of full scale wind turbine wakes, whether the objective is a better understanding of some features of the wake or the validation of wake models. Since these lidars are based on the Doppler effect, a single scanning lidar normally relies on certain assumptions when estimating some components of the wind velocity vector. Furthermore, in order to reconstruct volumetric information, one needs to aggregate data, perform statistics on it and, most likely, interpolate to a convenient coordinate system, all of which introduce uncertainty in the measurements. This study simulates the performance of a virtual lidar performing stacked step-and-stare plan position indicator (PPI) scans on large-eddy simulation (LES) data, reconstructs the wake in terms of the average and the standard deviation of the longitudinal velocity component, and quantifies the errors. The variables included in the study are as follows: the location of the lidar (ground-based and nacelle-mounted), different atmospheric conditions, and varying scan speeds, which in turn determine the angular resolution of the measurements. Testing different angular resolutions allows one to find an optimum that balances the different error sources and minimizes the total error. An optimum angular resolution of 3 ∘ has been found to provide the best results. The errors found when reconstructing the average velocity are low (less than 2% of the freestream velocity at hub height), which indicates the possibility of high quality field measurements with an optimal angular resolution. The errors made when calculating the standard deviation are similar in magnitude, although higher in relative terms than for the mean, thus leading to a poorer quality estimation of the standard deviation. This holds true for the different inflow cases studied and for both ground-based and nacelle-mounted lidars.
Trajectory-based Visual Analytics for Anomalous Human Movement Analysis using Social Media

The rapid development and increasing availability of mobile communication and location acquisition technologies allow people to add location data to existing social networks so that people share location-embedded information. For human movement analysis, such location-based social networks have been gaining attention as promising data sources. Researchers have mainly focused on ﬁnding daily activity patterns and detecting outliers. However, during crisis events, since the movement patterns are irregular, a new approach is required to analyze the movements. To address these challenges, we propose a trajectory-based visual analytics system for analyzing anomalous human movements during disasters using social media. We extract trajectories from location-based social networks and cluster the trajectories into sets of similar sub-trajectories in order to discover common human movement patterns. We also propose a classiﬁcation model based on historical data for detecting abnormal movements using human expert interaction.
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies used by different protocols and exploit this information for quality assessment at the sample-level and provide effective visualization of these results in preparation for higher-level analyses. To this end, we developed scPipe, an R/Bioconductor package that integrates barcode demultiplexing, read alignment, UMI-aware gene-level quantification and quality control of raw sequencing data generated by multiple protocols that include CEL-seq, MARS-seq, Chromium 10X, Drop-seq and Smart-seq. scPipe produces a count matrix that is essential for downstream analysis along with an HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing. scPipe performs this processing in a few simple R commands, promoting reproducible analysis of single-cell data that is compatible with the emerging suite of open-source scRNA-seq analysis tools available in R/Bioconductor and beyond. The scPipe R package is available for download from https://www.bioconductor. org/packages/scPipe.
An Interactive Visual Representation to Explore Association with Hierarchical Social Circles

Showing the relations between the contacts of an ego network, a subset of a large social network, and these contacts’ associations to different social circles enables us exploring inside behavior of the underlying ego network. Normally, these social circles contain multiple hierarchies in them and many times the social circles at the second or lower level in the hierarchy are non-mutually exclusive. In this work, we propose an intuitive design solution to visualize an ego network with associated social circles, where the inside Chord diagram represents the contacts and their relations in an ego network while the outside arcs represent the associated social circles, keeping their hierarchies and the non-mutually exclusive property. Our HiSoC-Vis tool provides a number of interaction and ﬁltering options to make the resulting visualization more intuitive and customizable.
Coalescence and Linkage Disequilibrium in Facultatively Sexual Diploids

Under neutrality, linkage disequilibrium results from physically linked sites having nonindependent coalescent histories. In obligately sexual organisms, meiotic recombination is the dominant force separating linked variants from one another, and thus in determining the decay of linkage disequilibrium with physical distance. In facultatively sexual diploid organisms that principally reproduce clonally, mechanisms of mitotic exchange are expected to become relatively more important in shaping linkage disequilibrium. Here we outline mathematical and computational models of a facultative-sex coalescent process that includes meiotic and mitotic recombination, via both crossovers and gene conversion, to determine how linkage disequilibrium is affected with facultative sex. We demonstrate that the degree to which linkage disequilibrium is broken down by meiotic recombination simply scales with the probability of sex if it is sufficiently high (much greater than 1/N for population size N). However, with very rare sex (occurring with frequency on the order of 1/N), mitotic gene conversion plays a particularly important and complicated role because it both breaks down associations between sites and removes within-individual diversity. Strong population structure under rare sex leads to lower average linkage disequilibrium values than in panmictic populations, due to the influence of low-frequency polymorphisms created by allelic sequence divergence acting in individual subpopulations. These analyses provide information on how to interpret observed linkage disequilibrium patterns in facultative sexuals and to determine what genomic forces are likely to shape them.
Does a Supplemental Low-Protein Diet Decrease Mortality and Adverse Events After Commencing Dialysis? A Nationwide Cohort Study

Background: A beneficial effect of a ketoanalogue-supplemented low-protein diet (sLPD) in postponing dialysis has been demonstrated in numerous previous studies. However, evidence regarding its effect on long-term survival is limited. Our study assessed the long-term outcomes of patients on an sLPD after commencing dialysis. Methods: This retrospective study examined patients with new-onset end-stage renal disease with permanent dialysis between 2001 and 2013, extracted from Taiwan’s National Health Insurance Research Database. Patients who received more than 3 months of sLPD treatment in the year preceding the start of dialysis were extracted. The outcomes studied were all-cause mortality, infection rate, and major cardiac and cerebrovascular events (MACCEs). Results: After propensity score matching, the sLPD group (n = 2607) showed a lower risk of all-cause mortality (23.1% vs. 27.6%, hazard ratio (HR) 0.77, 95% confidence interval (CI) 0.70–0.84), MACCEs (19.2% vs. 21.5%, HR 0.86, 95% CI 0.78–0.94), and infection-related death (9.9% vs. 12.5%, HR 0.76, 95% CI 0.67–0.87) than the non-sLPD group did. Conclusion: We found that sLPD treatment might be safe without long-term negative consequences after dialysis treatment.
The Therapeutic Strategy of HDAC6 Inhibitors in Lymphoproliferative Disease

Histone deacetylases (HDACs) are master regulators of chromatin remodeling, acting as epigenetic regulators of gene expression. In the last decade, inhibition of HDACs has become a target for specific epigenetic modifications related to cancer development. Overexpression of HDAC has been observed in several hematologic malignancies. Therefore, the observation that HDACs might play a role in various hematologic malignancies has brought to the development of HDAC inhibitors as potential antitumor agents. Recently, the class IIb, HDAC6, has emerged as one potential selective HDACi. This isoenzyme represents an important pharmacological target for selective inhibition. Its selectivity may reduce the toxicity related to the off-target effects of pan-HDAC inhibitors. HDAC6 has also been studied in cancer especially for its ability to coordinate a variety of cellular processes that are important for cancer pathogenesis. HDAC6 has been reported to be overexpressed in lymphoid cells and its inhibition has demonstrated activity in preclinical and clinical study of lymphoproliferative disease. Various studies of HDAC6 inhibitors alone and in combination with other agents provide strong scientific rationale for the evaluation of these new agents in the clinical setting of hematological malignancies. In this review, we describe the HDACs, their inhibitors, and the recent advances of HDAC6 inhibitors, their mechanisms of action and role in lymphoproliferative disorders.
Vinflunine in the treatment of bladder cancer

Vinflunine (VFL) is a third-generation bifluorinated semi-synthetic vinca alkaloid obtained by superacidic chemistry from its parent compound, vinorelbine. As with the other vinca alkaloids, the main antineoplastic effects of VFL arise from its interaction with tubulin, the major component of microtubules in mitotic spindles. In contrast to other vinca alkaloids, VFL shows some distinctive properties in terms of tubulin binding, possibly explaining its superior antitumor activity in vitro and in vivo compared with vinorelbine as well as its excellent safety profile. In transitional cell carcinoma (TCC), two single-agent phase II trials were performed testing VFL in platinum-pretreated patients, showing moderate response rates and promising disease control rates. Therefore, the first phase III trial in modern times for second-line TCC of the urothelium was designed in order to further investigate the activity of VFL. First results were presented at the 2008 ASCO conference. VFL appears to be a possible treatment option for patients with TCC progressing after first-line platinum-containing chemotherapy.
Amino-acid-enriched cereals ready-to-use therapeutic foods (RUTF) are as effective as milk-based RUTF in recovering essential amino acid during the treatment of severe acute malnutrition in children: An individually randomized control trial in Malawi

Background Ready-to-use therapeutic food (RUTF) is used to treat children suffering from severe acute malnutrition (SAM). Standard RUTF uses milk as the primary protein source, which makes the product expensive, and given the high worldwide SAM burden, having a less expensive effective alternative is a public health priority. Objective The objective of this study was to evaluate whether newly developed amino acid-enriched milk-free RUTF (FSMS-RUTF) or amino acid-enriched low-milk RUTF (MSMS-RUTF) treatment could replenish plasma amino acids to levels comparable to those following standard peanut-milk RUTF (PM-RUTF) treatment and to improve understanding of the effects of treatment on anthropometric measurements. A secondary analysis was performed to test the noninferiority hypothesis of plasma essential amino acid (EAA) levels. Methods Plasma EAA levels were measured in a nonblinded, 3-arm, parallel-group simple randomized controlled trial conducted in Malawi to examine the efficacy of FSMS-RUTF, MSMS-RUTF and PM-RUTF in the treatment of SAM in 2 groups of children aged 6–23 and 24–59 months (mo). Sample size calculations were performed based on the previous our study. A noninferiority margin was set at -25% of the PM-RUTF arm at discharge. Results The relative values of the differences (95% CI) in plasma EAA levels between PM-RUTF treatment and FSMS-RUTF and MSMS-RUTF treatments at discharge were -7.9% (-18.6, 2.8) and 9.8% (0.2, 19.5), respectively, in children aged 6–23 mo, while in those aged 24–59 mo, the difference values were 17.8% (1.6, 34.1) and 13.6% (-2.8, 29.9), respectively. Conclusion At discharge, the plasma EAA concentrations in 6-59-mo-old SAM children treated with FSMS-RUTF and MSMS-RUTF were not less than those of children treated with PM-RUTF. These findings indicate that treatment with either of the 3 RUTFs was associated with adequate protein synthesis and that all the formulations provided sufficient functional metabolites of plasma amino acids to support nutritional recovery from SAM.
Characterization of Antibacterial Cell-Free Supernatant from Oral Care Probiotic Weissella cibaria, CMU

Recently, studies have explored the use of probiotics like the Weissella cibaria strain, CMU (oraCMU), for use as preventive dental medicine instead of chemical oral care methods. The present study was conducted to investigate the antibacterial properties of the cell-free supernatant (CFS) from this bacterium. Cell morphology using the scanning electron microscope, and the antibacterial effect of CFS under various growth conditions were evaluated. The production of hydrogen peroxide, organic acids, fatty acids, and secretory proteins was also studied. Most of the antibacterial effects of oraCMU against periodontal pathogens were found to be acid- and hydrogen peroxide-dose-dependent effects. Lactic acid, acetic acid, and citric acid were the most common organic acids. Among the 37 fatty acids, only 0.02% of oleic acid (C18:1n-9, cis) was detected. Proteomic analysis of the oraCMU secretome identified a total of 19 secreted proteins, including N-acetylmuramidase. This protein may be a potential anti-microbial agent effective against Porphyromonas gingivalis.
Interactions of organic acids with Campylobacter coli from swine

Campylobacter coli is a bacterial species that is a major cause of diarrheal disease worldwide, and Campylobacter spp. are among the top 5 foodborne pathogens in the United States. During food production organic acids (OAs) are often used to remove bacteria from animal carcasses. The interactions of six OAs with 111 C. coli strains obtained from swine and retail pork chops were studied by determining the molar minimum inhibitory concentrations (MICMs) of the C. coli strains, and the pH at the MICMs. The Henderson-Hasselbalch equation was used to calculate the concentrations of the undissociated and dissociated OAs at the MICMs of the C. coli strains. The results for the 111 different C. coli strains obtained from different locations were treated as a single group for each OA since many of the C. coli strains behaved similarly to each different OA. Inhibition of C. coli was not dependent on pH or on the undissociated OA species, but C. coli inhibition correlated with the dissociated OA species. Therefore, if the concentration of the dissociated OAs decreases from optimum, one may then expect that C. coli bacteria would escape disinfection. The concentration of the dissociated OA should be carefully controlled in a carcass wash. We suggest maintaining a concentration of the dissociated acetic, butyric, citric, formic, lactic and propionic acids at 29, 23, 11, 35, 22 and 25 mM, respectively, when using a carcass wash with these OAs to remove C. coli bacteria. However, due to C. coli utilization of acetate, formate, lactate and propionate, these four OAs may not be the best choice to use for a carcass wash to remove C. coli contamination. Of the six OAs, citric acid was the most efficient at inhibiting C. coli.