Miracle-dz/UniFAR-FTUs huggingface dataset:
High‐throughput sequencing of T‐cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid malignancies

Rearrangements of T‐ and B‐cell receptor (TCR and BCR) genes are useful markers for clonality assessment as well as for minimal residual disease (MRD) monitoring during the treatment of haematological malignancies. Currently, rearrangements of three out of four TCR and all BCR loci are used for this purpose. The fourth TCR gene, TRA, has not been used so far due to the lack of a method for its rearrangement detection in genomic DNA. Here we propose the first high‐throughput sequencing based method for the identification of clonal TRA gene rearrangements at the DNA level. The method is based on target amplification of the rearranged TRA locus using an advanced multiplex polymerase chain reaction system and high‐throughput sequencing, and has been tested on DNA samples from peripheral blood of healthy donors. Combinations of all functional V‐ and J‐segments were detected, indicating the high sensitivity of the method. Additionally, we identified clonal TRA rearrangements in 57 out of 112 tested DNA samples of patients with various T‐lineage lymphoproliferative disorders. The method fills the existing gap in utilizing the TRA gene for a wide range of studies, including clonality assessment, MRD monitoring and clonal evolution analysis in different lymphoid malignancies.
The Structure of Design Orientation and its Relationship with Market Orientation

Abstract Although market orientation has been investigated in numerous studies, its complex relationship with design orientation lacks research attention, especially in countries with transitional economies. Therefore, existing models of market orientation (MO) and design orientation (DO) have been investigated. The research has been executed in several stages, combining qualitative and quantitative methods. In the first, qualitative stage, a series of face-to-face in-depth interviews were conducted. In the second, quantitative stage, an Internet survey was conducted among managers and CEOs from Croatian companies in different industries. Partial Least Square and Structural Equation Modelling analyses were conducted to examine the relationships between variables of MO and DO. Results confirm the positive relationship between design orientation and market orientation. Further, results also confirm sub-hypotheses that customer orientation and strategic marketing are positively related to all dimensions of design orientation. The model could have implications for marketers, designers and managers in practice. Both concepts, MO and DO, are very complex and multidimensional, so it was not possible to investigate all the aspects of the constructs. Another limitation of the study was the sample size, as a result of a low response rate as well as a relatively high drop-out rate. The research contributes to theory highlighting the role of design as an important element of market orientation.
T12 Dorsal Root Ganglion Stimulation to Treat Chronic Low Back Pain: A Case Series

Dorsal root ganglion stimulation (DRG‐S) is a neuromodulation technique for treating neuropathic pain syndromes. Research has demonstrated DRG‐S to be more effective than conventional SCS in treating RSD/CRPS, particularly of the lower extremities. Results from recent case series and prospective studies suggest that DRG‐S may be effective in treatment of pain syndromes considered to have non‐neuropathic components and characteristics (e.g. nociceptive). There have been multiple, small studies demonstrating efficacy of DRG‐S for axial low back pain. There has, however, been no consensus regarding the best location for DRG lead placement in the treatment of low back pain.
Déjà vu and prescience in a case of severe episodic amnesia following bilateral hippocampal lesions

ABSTRACT Several studies pertaining to déjà vu have consistently made a connection with the perirhinal region, a region located below the hippocampus. This idea is strengthened by the fact that déjà vu is an erroneous sense of familiarity and that familiarity appears to largely depend on the perirhinal region in healthy subjects. In this context, the role of the hippocampus is particularly unclear as it is unknown whether or not it plays a role in the genesis of déjà vu. We report on the case of OHVR, an epileptic patient who suffers from severe episodic amnesia related to massive isolated bilateral damage to the hippocampus. In contrast, the perirhinal region is intact structurally and functionally. This patient reports frequent déjà vu but also another experiential phenomenon with a prominent feeling of prescience, which shows some of the characteristics of déjà vécu. She clearly distinguishes both. She also developed a form of synaesthesia by attributing affective valence to numbers. This study shows that déjà vu can occur in cases of amnesia with massively damaged hippocampi and confirms that the perirhinal region is a core region for déjà vu, using a different approach from previous reports. It also provides clues about a potential influence of hippocampal alterations in déjà vécu.
International Normalized Ratio as a Screening Test for Assessment of Anticoagulant Activity for Patients Treated With Rivaroxaban or Apixaban: A Pilot Study

Introduction: In patients treated with direct oral anti activated factor X (anti-FXa) anticoagulants such as apixaban and rivaroxaban, there are several emergency and non-emergency conditions in which anticoagulation activity should be measured. The validity of the common global clotting tests, prothrombin time and international normalized ratio (PT/INR) for determination of blood levels of these drugs, has been widely investigated. As the anticoagulation activity evaluation “calibrated anti-FXa” of these drugs is relatively more expensive and less available, we aimed to build a prediction model for anticoagulation activity assessment based on INR values. Methods and Findings: One hundred sixty samples from 80 hospitalized patients treated with apixaban or rivaroxaban were tested using PT/INR and Anti-FXa chromogenic assay. Two blood samples, trough and peak, were collected from each subject. Participants were randomly divided into two equal groups. One group (n = 40) was used to build the model, which was validated by the second group (n = 40). There was a strong correlation between anti-FXa concentrations and INR in rivaroxaban treated patients (r = 0.899, p < 0.001). Therefore, we were able to build a formula for rivaroxaban patient group which reliably represent the relationship between these two parameters. The correlation in apixaban treated patients was less predictive (r = 0.798, p < 0.001) and the formula suggested could not be validated. Conclusions: In our study, we developed a formula that estimates the anticoagulant activity of rivaroxaban by obtaining INR values. Where anti-FXa assay is unavailable, our proposed formula may be considered as a screening test for rivaroxaban.
Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha−1. Soil samples were collected at a 0–15 cm depth from 2016–2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.
Study on the synthesis of hexene-1 catalyzed by Ziegler-Natta catalyst and polyhexene-1 applications

Abstract This paper presents the synthesis of two aminosilane-based external donors for the Ziegler-Natta catalysis: di(piperidyl) dimethoxysilane (DPPDMS) and dipyrrolyldimethoxysilane (DPRDMS). We compared the electron donation by these two compounds in the MgCl2- supported Ziegler-Natta catalysis of the polymerization of hexene-1 into a polyhexene-1 (PHe) elastomer with that of the common donor cyclohexylmethyldimethoxysilane (CHMMS). The catalytic activity of the system and isotacticity of the polymer (PHe) product improved significantly because of the considerable steric hindrance and strong electronic effects of these aminosilane-based external donors. The effects of different external donors on the catalytic efficiency, polymer isotacticity, molecular weight and molecular weight distribution of the PHe products were investigated. Under the best reaction conditions, the catalyst activity, polymer molecular weight, and glass-transition temperature were determined as 899 g/g Cat·h-1, MW = 252,300 g/mol, and -41.39°C, respectively. The PHe was characterized by FTIR and NMR. This report also describes blending of PHe and low density polyethylene that leads to a significant increase in the impact strength and elongation at breaks.
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions

Abstract Summary Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization. Availability and implementation phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize. Supplementary information Supplementary data are available at Bioinformatics online.
Retention in care and factors critical for effectively implementing antiretroviral adherence clubs in a rural district in South Africa

Differentiated models of care that include referral of antiretroviral treatment (ART) clients to adherence clubs are an important strategy to help clinics manage increased number of clients living with HIV in resource‐constrained settings. This study reported on (i) clinical outcomes among ART clients attending community‐based adherence clubs and (ii) experiences of adherence clubs and perceptions of factors key to successful adherence club implementation among clients and healthcare workers.
Neurourology and Urodynamics

Funding information Research contract between the University of Auckland, New Zealand and Université de Montréal, Canada Abstract Aims: To test the reliability and validity of intravaginal pressure measurements acquired during pelvic floor muscle (PFM) tasks in different body positions using the FemFit®, a new intravaginal pressure device. Methods: Twenty healthy adult women participated in this study. Two assessment sessions were conducted. Intravaginal pressure measurements using the FemFit® were repeated during PFM contraction and straining maneuvers while lying and standing. Maximal intravaginal pressures were collated and compared within and between sessions. They were also correlated to maximal force measurements obtained by dynamometry and vaginal digital palpation. Test‐retest reliability was assessed using intraclass correlation coefficient, standard error of measurement and Bland‐Altman plots. The validity of the pressure measurements was assessed using Pearson’s correlation (dynamometry) and Spearman’s rho (palpation). Results: This test‐retest study indicate excellent reliability for PFM contraction and straining maneuver both in lying and standing, within and between sessions. For the straining maneuver while standing, increased variability was suggested by a wider limit of agreement on Bland‐Altman plots (spanning 31.3 to 43.3mm Hg). A significant moderate to strong correlation was found when comparing measurements of PFM contraction using the FemFit® and the dynamometer or the palpation (Pearson’s coefficient = 0.72, P= .006; Spearman’s rho = 0.68, P= .005, respectively). Conclusion: Our research findings suggest that intravaginal pressures can be reliably measured during PFM contraction and straining manoeuver while lying and standing, using the FemFit® device, both within and between sessions. A moderate to strong correlation between the FemFit® pressure and the force measurements obtained by dynamometry or palpation reinforce the validity of measurements.
Use of a Web-Based Dietary Assessment Tool (RiksmatenFlex) in Swedish Adolescents: Comparison and Validation Study

Background A Web-based dietary assessment tool—RiksmatenFlex—was developed for the national dietary survey of adolescents in Sweden. Objective This study aimed to describe the Web-based method RiksmatenFlex and to test the validity of the reported dietary intake by comparing dietary intake with 24-hour dietary recalls (recall interviews), estimated energy expenditure, and biomarkers. Methods Adolescents aged 11-12, 14-15, and 17-18 years were recruited through schools. In total, 78 students had complete dietary information and were included in the study. Diet was reported a few weeks apart with either RiksmatenFlexDiet (the day before and a random later day) or recall interviews (face-to-face, a random day later by phone) in a cross-over, randomized design. At a school visit, weight and height were measured and blood samples were drawn for biomarker analyses. Students wore an accelerometer for 7 days for physical activity measurements. Dietary intake captured by both dietary methods was compared, and energy intake captured by both methods was compared with the accelerometer-estimated energy expenditure (EEest). Intake of whole grain wheat and rye and fruit and vegetables by both methods was compared with alkylresorcinol and carotenoid concentrations in plasma, respectively. Results The mean of the reported energy intake was 8.92 (SD 2.77) MJ by RiksmatenFlexDiet and 8.04 (SD 2.67) MJ by the recall interviews (P=.01). Intake of fruit and vegetables was 224 (169) g and 227 (150) g, and whole grain wheat and rye intake was 12.4 (SD 13.2) g and 12.0 (SD 13.1) g, respectively; the intakes of fruit and vegetables as well as whole grain wheat and rye did not differ between methods. Intraclass correlation coefficients ranged from 0.57 for protein and carbohydrates to 0.23 for vegetables. Energy intake by RiksmatenFlexDiet was overreported by 8% (P=.03) but not by the recall interviews (P=.53) compared with EEest. The Spearman correlation coefficient between reported energy intake and EEest was 0.34 (P=.008) for RiksmatenFlexDiet and 0.16 (P=.21) for the recall interviews. Spearman correlation coefficient between whole grain wheat and rye and plasma total alkylresorcinol homologs was 0.36 (P=.002) for RiksmatenFlexDiet and 0.29 (P=.02) for the recall interviews. Spearman correlations between intake of fruit and vegetables and plasma carotenoids were weak for both dietary tools. The strongest correlations were observed between fruit and vegetable intake and lutein/zeaxanthin for RiksmatenFlexDiet (0.46; P<.001) and for recall interviews (0.28; P=.02). Conclusions RiksmatenFlexDiet provides information on energy, fruit, vegetables, and whole grain wheat and rye intake, which is comparable with intake obtained from recall interviews in Swedish adolescents. The results are promising for cost-effective dietary data collection in upcoming national dietary surveys and other studies in Sweden. Future research should focus on how, and if, new technological solutions could reduce dietary reporting biases.
Fast and unbiased purification of RNA-protein complexes after UV cross-linking

Post-transcriptional regulation of gene expression in cells is facilitated by formation of RNA-protein complexes (RNPs). While many methods to study eukaryotic (m)RNPs rely on purification of poly-adenylated RNA, other important regulatory RNA classes or bacterial mRNA could not be investigated at the same depth. To overcome this limitation, we developed PTex (Phenol Toluol extraction), a novel and unbiased method for the purification of UV cross-linked RNPs in living cells. PTex is a fast (2-3 hrs) low-tech protocol; its purification principle is solely based on physicochemical properties of cross-linked RNPs. This enables us now for the first time to interrogate RNA-protein interactions system-wide and beyond poly-A-RNA from a variety of species and source material. Here, we are presenting an introduction of the underlying separation principles and give a detailed discussion of the individual steps as well as utilisation of PTex in high-throughput pipelines.
Molecular interaction balanced one- and two-dimensional hybrid nanoarchitectures for high-performance supercapacitors.

Hybridisation of one-dimensional (1D) and two-dimensional (2D) materials to enhance charge storage has received considerable attention, but a fundamental understanding of the inherent ratio-dependent charge transfer mechanisms associated with the modulation of their molecular interactions is still within the community. Herein, we examined 1D surface oxidised carbon nanotubes (Ox-CNTs) and 2D reduced graphene oxide (rGO) to understand their ratio-dependent charge transfer and molecular interaction dynamics. We found that stepwise ultrasonication and the self-assembly process can control the thermodynamic molecular interactions, which result in rGO and Ox-CNT suspensions not only well dispersed in N,N-dimethylformamide but also self-organised into sandwiched nanoarchitectures. We reveal that the enhanced charge storage performance originated from the Ox-CNT-mediated low contact resistance between the active material and the current collector, and the incorporation of rGO leads to a significant ion diffusion coefficient and gives rise to numerous ion diffusion channels for high rate retention. Through a systematic electrochemical characterisation, we found that the GC5 : 5 hybrids (mass ratio of rGO to Ox-CNT) provide the best compromise-balance ratio between rGO and Ox-CNT for realising a champion energy density (9 W h kg-1) and power density (10 kW kg-1) beyond the state-of-the-art performance of the individual materials. Our results herald the advent of molecular level hybridisation of 1D-2D materials for high-performance electrochemical energy storage.
An exploration of gender-based violence in eastern Myanmar in the context of political transition: findings from a qualitative sexual and reproductive health assessment

Abstract In March 2011, the Myanmar Government transitioned to a nominally civilian parliamentary government, resulting in dramatic increases in international investments and tenuous peace in some regions. In March 2015, Community Partners International, the Women’s Refugee Commission, and four community-based organisations (CBOs) assessed community-based sexual and reproductive health (SRH) services in eastern Myanmar amidst the changing political contexts in Myanmar and Thailand. The team conducted 12 focus group discussions among women of reproductive age (18–49 years) with children under five and interviewed 12 health workers in Kayin State, Myanmar. In Mae Sot and Chiang Mai, Thailand, the team interviewed 20 representatives of CBOs serving the border regions. Findings are presented through the socioecological lens to explore gender-based violence (GBV) specifically, to examine continued and emerging issues in the context of the political transition. Cited GBV includes ongoing sexual violence/rape by the military and in the community, trafficking, intimate partner violence, and early marriage. Despite the political transition, women continue to be at risk for military sexual violence, are caught in the burgeoning economic push–pull drivers, and experience ongoing restrictive gender norms, with limited access to SRH services. There is much fluidity, along with many connections and interactions among the contributing variables at all levels of the socioecological model; based on a multisectoral response, continued support for innovative, community-based SRH services that include medical and psychosocial care are imperative for ethnic minority women to gain more agency to freely exercise their SR rights.
Document Recovery from Bag-of-Word Indices

Motivated by computer privacy issues, we present the novel problem of document recovery from an index: given only a document’s bag-of-words (BOW) vector or other type of index, reconstruct the original ordered document. We investigate a variety of index types, including count-based BOW vectors, stopwords-removed count BOW vectors, indicator BOW vectors, and bigram count vectors. We formulate the problem as hypothesis rescoring using A ∗ search with the Google Web 1T 5-gram corpus. Our experiments on ﬁve domains indicate that if original documents are short, the documents can be recovered with high accuracy.