bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hera-T: an efficient and accurate approach for quantifying gene abundances from 10X-Chromium data with high rates of non-exonic reads
Authors: Tran Thang , Truong Thao , Vuong Hy , Pham Son 
Published: January 2019

AbstractAn important but rarely discussed phenomenon in single cell data generated by the 10X-Chromium protocol is that the fraction of non-exonic reads is very high. This number usually exceeds 30% of the total reads. Without aligning them to a complete genome reference, non-exonic reads can be erroneously aligned to the transcriptome reference with higher error rates. To tackle this problem, Cell Ranger chooses to firstly align reads against the whole genome, and at a later step, uses a genome annotation to select reads that align to the transcriptome. Despite its high running time and large memory consumption, Cell Ranger remains the most widely used tool to quantify 10XGenomics single cell RNA-Seq data for its accuracy.In this work, we introduce Hera-T, a fast and accurate tool for estimating gene abundances in single cell data generated by the 10X-Chromium protocol. By devising a new strategy for aligning reads to both transcriptome and genome references, Hera-T reduces both running time and memory consumption from 10 to 100 folds while giving similar results compared to Cell Ranger’s. Hera-T also addresses some difficult splicing alignment scenarios that Cell Ranger fails to address, and therefore, obtains better accuracy compared to Cell Ranger. Excluding the reads in those scenarios, Hera-T and Cell Ranger results have correlation scores > 0.99.For a single-cell data set with 49 million of reads, Cell Ranger took 3 hours (179 minutes) while Hera-T took 1.75 minutes; for another single-cell data set with 784 millions of reads, Cell Ranger took about 25 hours while Hera-T took 32 minutes. For those data sets, Cell Ranger completely used all 32 GB of memory while Hera-T consumed at most 8 GB. Hera-T package is available for download at: https://bioturing.com/product/hera-t
Engineered reversal of function in glycolytic yeast promoters
Authors: Rajkumar Arun S. , Özdemir Emre , Lis Alicia V. , Schneider Konstantin , Jensen Michael K. , Keasling Jay D. 
Published: January 2019

ABSTRACTPromoters are key components of cell factory design, allowing precise expression of genes in a heterologous pathway. Several commonly-used promoters in yeast cell factories belong to glycolytic genes, highly expressed in actively-growing yeast when glucose is used as a carbon source. However, their expression can be suboptimal when alternate carbon sources are used, or if there is a need to decouple growth from production. Hence, there is a need for alternate promoters for different carbon sources and production schemes. In this work, we demonstrate a reversal of regulatory function in two glycolytic yeast promoters by replacing glycolytic regulatory elements with ones induced by the diauxic shift. We observe a shift in induction from glucose-rich to glucose-poor medium without loss of regulatory activity, and strong ethanol induction. Applications of these promoters were validated for expression of the vanillin biosynthetic pathway, reaching production of vanillin comparable to pathway designs using strong constitutive promoters.
“Risk Factors for Visceral Leishmaniasis in Selected High Endemic Areas of Morang District, Nepal”: A case control study
Authors: Mandal Punam Kumari , Wagle Rajendra Raj , Thakur Ajoy Kumar , Uranw Surendra 
Published: January 2019

AbstractVisceral leishmaniasis is a major public health concern in Nepal. During the last few years, several KA outbreaks have been reported from Tarai region including Morang district. A case control study was conducted to assess the risk factors associated with VL in 5 endemic VDC of Morang district with 62 cases already treated from BPKIHS and Koshi zonal hospital and 248 controls selected randomly from the same village. Data collected using semi structured questionnaire from September to November 2013. This study revealed that people living in thatched house, sleeping in ground floor, ownership of animal, history of migration to India (Bihar and Jharkhand) and proximity to other KA cases within 50 m distance of household were strong risk factors for VL. Education remains protective (OR 0.39,95 % CI 0.19-0.79). The association with socioeconomic status showed clear dose – response effect. The odds for VL consistently decreased as the level of socioeconomic status increased (OR 4.26, 3.81). Strengthening surveillance system for early diagnosis and treatment, awareness programme and further extensive study is needed on risk factor, vector and control measures.Author SummaryThis study aims to explore the risk factors for visceral leishmaniasis. Based on findings there is a need to educate people in high-transmission areas how to realize, reduce or avoid environmental factors that favor the survival of the vector in the community. Similarly introduction of more exact surveillance tools in order to improve morbidity and mortality surveillance by health sector. People living in mud thatched houses need to be aware about cracks and crevices in the mud walls, their function as breeding places and how they can be controlled, for example by plastering with lime and mud․. However, a primary condition is that people need to understand the purpose of all these efforts in order to be motivated to put them into practice.
A Short Bout of High-intensity Exercise Alters Ipsilesional Motor Cortical Excitability Post-stroke
Authors: Li Xin , Charalambous Charalambos C. , Reisman Darcy S. , Morton Susanne M. 
Published: January 2019

AbstractBackgroundAcute exercise can increase motor cortical excitability and enhance motor learning in healthy individuals, an effect known as exercise priming. Whether it has the same effects in people with stroke is unclear.ObjectivesThe objective of this study was to investigate whether a short, clinically-feasible high-intensity exercise protocol can increase motor cortical excitability in non-exercised muscles of chronic stroke survivors.MethodsThirteen participants with chronic, unilateral stroke participated in two sessions, at least one week apart, in a crossover design. In each session, they underwent either high-intensity lower extremity exercise or quiet rest. Motor cortical excitability of the extensor carpi radialis muscles was measured bilaterally with transcranial magnetic stimulation before and immediately after either exercise or rest. Motor cortical excitability changes (post-exercise or rest measures normalized to pre-test measures) were compared between exercise vs. rest conditions.ResultsAll participants were able to reach the target high-intensity exercise level. Blood lactate levels increased significantly after exercise (p < 0.001, d = 2.85). Resting motor evoked potentials from the lesioned hemisphere increased after exercise compared to the rest condition (p = 0.046, d = 2.76), but this was not the case for the non-lesioned hemisphere (p = 0.406, d = 0.25).ConclusionsHigh-intensity exercise can increase lesioned hemisphere motor cortical excitability in a non-exercised muscle post-stroke. Our short and clinically-feasible exercise protocol shows promise as a potential priming method in stroke rehabilitation.
Phylogeny of Holarctic gall wasps of the genera Diplolepis and Periclistus (Hymenoptera: Cynipidae) based on DNA barcodes
Authors: Zhang Y. Miles , László Zoltán , Looney Chris , Dénes Avar-Lehel , Hanner Robert H. , Shorthouse Joseph D. 
Published: January 2019

AbstractRose gall wasps Diplolepis induce structurally distinct galls on wild roses, which provide gallers with food and shelter. These galls are attacked by a wide variety of micro-hymenopterans including another cynipid Periclistus that act as inquilines. Both Diplolepis and Periclistus are difficult to distinguish based on adult morphology, instead the structural appearance of galls is often used to distinguish species. Using the mitochondrial gene COI, we built phylogenies of both Diplolepis and Periclistus, while also estimating the ancestral host use of the inducers. Our phylogeny recovered the monophyly of Diplolepis, which have likely diverged from single-or multi-chambered leaf gallers to other plant organs. Periclistus exhibits a divide between the Palearctic and Nearctic clades, and ranges from specialists to generalists in terms of host specificity. The molecular results have largely supported the validity of species described in the literature, with notable exceptions in four species groups. While it is premature to enact any taxonomic changes without additional molecular markers, this incongruence between morphological and molecular data indicates these groups need taxonomic revision and gall morphology alone may be inadequate to delimit species.
Factorial Mendelian randomization: using genetic variants to assess interactions
Authors: Rees Jessica MB , Foley Christopher N , Burgess Stephen 
Published: January 2019

AbstractBackgroundFactorial Mendelian randomization is the use of genetic variants to answer questions about interactions. Although the approach has been used in applied investigations, little methodological advice is available on how to design or perform a factorial Mendelian randomization analysis. Previous analyses have employed a 2 × 2 approach, using dichotomized genetic scores to divide the population into 4 subgroups as in a factorial randomized trial.MethodsWe describe two distinct contexts for factorial Mendelian randomization: investigating interactions between risk factors, and investigating interactions between pharmacological interventions on risk factors. We propose two-stage least squares methods using all available genetic variants and their interactions as instrumental variables, and using continuous genetic scores as instrumental variables rather than dichotomized scores. We illustrate our methods using data from UK Biobank to investigate the interaction between body mass index and alcohol consumption on systolic blood pressure.ResultsSimulated and real data show that efficiency is maximized using the full set of interactions between genetic variants as instruments. In the applied example, between four- and ten-fold improvement in efficiency is demonstrated over the 2 × 2 approach. Analyses using continuous genetic scores are more efficient than those using dichotomized scores. Efficiency is improved by finding genetic variants that divide the population at a natural break in the distribution of the risk factor, or else divide the population into more equal sized groups.ConclusionsPrevious factorial Mendelian randomization analyses may have been under-powered. Efficiency can be improved by using all genetic variants and their interactions as instrumental variables, rather than the 2 × 2 approach.Key messagesFactorial Mendelian randomization is an extension of the Mendelian randomization paradigm to answer questions about interactions.There are two contexts in which factorial Mendelian randomization can be used: for investigating interactions between risk factors, and interactions between pharmacological interventions on risk factors.While most applications of factorial Mendelian randomization have dichotomized the population as in a 2 × 2 factorial randomized trial, this approach is generally inefficient for detecting statistical interactions.In the first context, efficiency is maximized by including all genetic variants and their cross-terms as instrumental variables for the two risk factors and their product term.In the second context, efficiency is maximized by using continuous genetic scores rather than dichotomized scores.
IFN-α and 5-Aza-2’-deoxycytidine enhance the anti-tumor efficacy of a dendritic- cell targeting MIP3a-Gp100-Trp2 DNA vaccine by affecting T-cell recruitment and tumor microenvironment gene expression
Authors: Gordy James T. , Luo Kun , Markham Richard B. 
Published: January 2019

ABSTRACTBackgroundThe chemokine MIP-3α (CCL20) binds to CCR6 found on immature dendritic cells. DNA vaccines fusing MIP-3α to melanoma-associated antigens have shown improved efficacy and immunogenicity in the B16F10 model. To optimize the therapy, our laboratory has added agents designed to overcome immunoregulatory mechanisms of the tumor microenvironment. Here, we report that the combination of type-I interferon therapy (IFNα) with 5-Aza-2’-deoxycitidine (Aza) profoundly enhanced the therapeutic anti-melanoma efficacy of a MIP-3α-Gp100-Trp2 DNA vaccine.MethodsThe current studies utilize the B16F10 syngeneic mouse melanoma model. The vaccine is administered intramuscularly (i.m.) followed by i.m. electroporation. Vaccinations are given thrice at one-week intervals beginning day 5 with CpG adjuvant given two days later as noted. Aza is given i.p. at 1mg/kg on days 5 and 12. IFNα therapy is given in a series of one high followed by three low doses, beginning on days 5 and 12. Tumor sizes, growth, and survival were all assessed. Tumor microenvironment gene expression levels were explored by qRT-PCR. Tumor-infiltrating lymphocytes (TILs) were assessed by stimulating the purified lymphocyte fraction of tumors with vaccine antigens followed by intracellular cytokine staining flow cytometry.ResultsWe demonstrate that the addition of IFNα and Aza treatments to mice vaccinated with the MIP-3α-Gp100-Trp2 vaccine has led to significantly reduced tumor burden and overall increases in mouse survival, increasing median survival by 39% over vaccine and 86% over controls. Importantly, this increase in efficacy was dependent on the presence of all three components: vaccine, IFNα, and Aza. The addition of Aza and IFNα to the vaccine increased T-cell tumor infiltration and altered the proportion of CD8+T-cells. Also, IFNα and vaccine induced durable changes in IFNα-stimulated gene transcription.ConclusionsEfficient targeting of antigen to immature dendritic cells with a chemokine-fusion vaccine offers a potential alternative approach to classic and dendritic cell based vaccines currently undergoing clinical investigation. Combining this approach with IFNα and Aza combination treatment significantly improved vaccine efficacy, with efficacy correlating with changes in TILs and in IFNα -stimulated gene expression. Further potential therapy optimization currently undergoing investigation offers promise for this line of investigation to become a novel melanoma therapy.
Efficacy for Anemia and Changes in Serum Ferritin Levels by Long‐Term Oral Iron Administration in Hemodialysis Patients
Authors: Daimon Shoichiro 
Published: January 2019

AbstractOral iron preparations are useful for the treatment of anemia in hemodialysis patients; however, long‐term changes in the iron dynamics and effects of anemia are unknown. Serum ferritin levels and erythropoietin‐stimulating agent (ESA)/hemoglobin (Hb) ratios were investigated for 750 days in the following four groups: patients treated with sodium ferrous citrate (SF) (de novo 50 mg/day and 150 mg/day switched from 50 mg/day) and patients treated with 1500 mg/day of ferric citrate (FC) (de novo and switched from 50 mg/day of SF). Compared with the other groups, serum ferritin levels increased less apparently with de novo 50 mg/day SF. ESA/Hb ratios did not change in groups switched from 50 mg/day SF. Conversely, in groups with de novo iron, ESA/Hb ratios decreased and ultimately reached the same levels in all groups. Although more iron results in higher serum ferritin levels, 50 mg/day SF has an equivalent effect for anemia treatment.
Tramadol as an adjunct to intra‐articular local anaesthetic infiltration in knee arthroscopy: a systematic review and meta‐analysis
Authors: Ryan Thomas , Hodge Anthony , Holyoak Rhys , Vlok Ruan , Melhuish Thomas , Binks Matthew , Hurtado Glenn , White Leigh 
Published: January 2019

BackgroundArthroscopic knee surgery is a common technique used in Australia. Post‐operative pain is common and can lead to delayed discharge and impair early mobilization. Use of local anaesthesia can reduce pain while avoiding systemic side effects. This systematic review and meta‐analysis aimed to establish the use of tramadol as an adjunct to intra‐articular local anaesthetic infiltration in knee arthroscopy in the current literature.MethodsTwo independent reviewers performed a systematic search of four databases, where 24 articles were identified with six studies (four high‐quality and two low‐quality randomized controlled trials), with a total of 334 patients were included for analysis. RevMan 5.3 software (The Nordic Cochrane Centre, Copenhagen, Denmark) was used to perform the data analysis. The studies included focused on outcomes such as pain scores, breakthrough analgesia, total analgesia, time to discharge and adverse events related to the use of tramadol as an adjunctive therapy.ResultsThis study found that using tramadol as an adjunct to intra‐articular local anaesthetic infiltration in arthroscopic knee surgery reduced post‐operative pain and increased time to breakthrough analgesia without an increase in side effects.ConclusionThis meta‐analysis suggests that tramadol is an efficacious adjunct for use in intra‐articular local anaesthetic infiltration following arthroscopic knee surgery.
Twenty‐eight‐day follow‐up of patch test reactions to p‐phenylenediamine and p‐phenylenediamine dihydrochloride: A multicentre study on behalf of the European Environmental and Contact Dermatitis Research Group
Authors: Young Ewa , Andersen Klaus E. , Bruze Magnus , Giménez‐Arnau Ana , Ross‐Hansen Katrine , Johansen Jeanne D. , Madsen Jakob Torp , Zimerson Erik , Svedman Cecilia 
Published: January 2019

BackgroundThere is an ongoing discussion on whether routinely patch testing with p‐phenylenediamine (PPD) 1.0% pet. is safe, owing to the risk of patch test sensitization. Late‐appearing patch test reactions may reflect patch test sensitization, but may also be attributable to a low degree of pre‐existing sensitization.ObjectivesTo follow the positive patch test reactions to PPD and its salt PPD dihydrochloride (PPD‐DHC) in order to characterize reaction patterns concerning time and dose in PPD‐sensitized individuals.MethodsVolunteers with previous reactions to PPD 1.0% were included and patch tested with PPD and PPD‐DHC in equimolar dilution series. There were then seven follow‐up visits over a period of 28 days.ResultsTwenty‐six volunteers completed the study, of whom 23 of 26 (88%) reacted to PPD 1.0%, and 69% reacted to PPD 0.32%. Altogether, 42% and 27% reacted to the corresponding equimolar concentrations of PPD‐DHC. After day 7, no new reactions were observed to any concentration tested, either of PPD or of PPD‐DHC.ConclusionNo late‐appearing reactions to PPD or PPD‐DHC were observed at any dose. There is a risk of missing contact allergy when the dose is decreased.
Stomoxys calcitrans, mechanical vector of virulent Besnoitia besnoiti from chronically infected cattle to susceptible rabbit
Authors: Sharif S. , Jacquiet P. , Prevot F. , Grisez C. , Raymond‐Letron I. , Semin M. O. , Geffré A. , Trumel C. , Franc M. , Bouhsira É. , Liénard E. 
Published: January 2019

AbstractCattle besnoitiosis caused by Besnoitia besnoiti (Eucoccidiorida: Sarcocystidae) is a re‐emerging disease in Europe. Its mechanical transmission by biting flies has not been investigated since the 1960s. The aim of this study was to re‐examine the ability of Stomoxys calcitrans (Diptera: Muscidae) to transmit virulent B. besnoiti bradyzoites from chronically infected cows to susceptible rabbits. Three batches of 300 stable flies were allowed to take an interrupted bloodmeal on chronically infected cows, followed by an immediate bloodmeal on three rabbits (Group B). A control group of rabbits and a group exposed to the bites of non‐infected S. calcitrans were included in the study. Blood quantitative polymerase chain reaction (qPCR) analyses, and clinical, serological and haematological surveys were performed in the three groups over 152 days until the rabbits were killed. Quantitative PCR analyses and histological examinations were performed in 24 tissue samples per rabbit. Only one rabbit in Group B exhibited clinical signs of the acute phase of besnoitiosis (hyperthermia, weight loss, regenerative anaemia and transient positive qPCR in blood) and was seroconverted. Parasite DNA was detected in four tissue samples from this rabbit, but no cysts were observed on histological examination. These findings indicate that S. calcitrans may act as a mechanical vector of B. besnoiti more efficiently than was previously considered.
Anatomical changes with needle length are correlated with leaf structural and physiological traits across fivePinusspecies
Authors: Wang Na , Palmroth Sari , Maier Christopher A. , Domec Jean‐Christophe , Oren Ram 
Published: January 2019

AbstractThe genusPinushas wide geographical range and includes species that are the most economically valued among forest trees worldwide. Pine needle length varies greatly among species, but the effects of needle length on anatomy, function, and coordination and trade‐offs among traits are poorly understood. We examined variation in leaf morphological, anatomical, mechanical, chemical, and physiological characteristics among five southern pine species:Pinus echinata,Pinus elliottii,Pinus palustris,Pinus taeda, andPinus virginiana. We found that increasing needle length contributed to a trade‐off between the relative fractions of support versus photosynthetic tissue (mesophyll) across species. From the shortest (7 cm) to the longest (36 cm) needles, mechanical tissue fraction increased by 50%, whereas needle dry density decreased by 21%, revealing multiple adjustments to a greater need for mechanical support in longer needles. We also found a fourfold increase in leaf hydraulic conductance over the range of needle length across species, associated with weaker upward trends in stomatal conductance and photosynthetic capacity. Our results suggest that the leaf size strongly influences their anatomical traits, which, in turn, are reflected in leaf mechanical support and physiological capacity.
Brown, Title IX and the impact of race and sex segregation on sports participation opportunities for Black females
Authors: Theune Felecia 
Published: January 2019

AbstractAlthough neither the 1954 Brown v. Board of Education of Topeka, Kansas decision nor Title IX of the Education Amendments Act (1972) specifically mentions sports participation, both antidiscrimination laws have changed the landscape of high school and college sports by granting Blacks and females increased access to athletic opportunities previously reserved for Whites males. Although Brown and Title IX are popular topics among research scholars, studies rarely consider the unique experiences of Black females, who unlike Black males and White females, occupy at least two subordinate social locations due to their race and gender. This article goes beyond the usual single axis of inquiry and examines the intersection of Brown and Title IX and, thus, the intersection of race and sex for Black females who inhabit a sports world dominated by Whites and males. Using existing literature to assess the implementation and effectiveness of Brown and Title IX independently before exploring their sociohistorical linkages and integrated effect on access to sports participation opportunities, the author finds that Black women and girls have been left out of the game.