bluuebunny/crossref_metadata_2025_split huggingface dataset:
PHi-C: deciphering Hi-C data into polymer dynamics
Authors: Shinkai Soya , Nakagawa Masaki , Sugawara Takeshi , Togashi Yuichi , Ochiai Hiroshi , Nakato Ryuichiro , Taniguchi Yuichi , Onami Shuichi 
Published: March 2020

Abstract
Genomes are spatiotemporally organized within the cell nucleus. Genome-wide chromosome conformation capture (Hi-C) technologies have uncovered the 3D genome organization. Furthermore, live-cell imaging experiments have revealed that genomes are functional in 4D. Although computational modeling methods can convert 2D Hi-C data into population-averaged static 3D genome models, exploring 4D genome nature based on 2D Hi-C data remains lacking. Here, we describe a 4D simulation method, PHi-C (polymer dynamics deciphered from Hi-C data), that depicts 4D genome features from 2D Hi-C data by polymer modeling. PHi-C allows users to interpret 2D Hi-C data as physical interaction parameters within single chromosomes. The physical interaction parameters can then be used in the simulations and analyses to demonstrate dynamic characteristics of genomic loci and chromosomes as observed in live-cell imaging experiments. PHi-C is available at https://github.com/soyashinkai/PHi-C.
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions
Authors: Kuksa Pavel P , Amlie-Wolf Alexandre , Hwang Yih-Chii , Valladares Otto , Gregory Brian D , Wang Li-San 
Published: March 2020

Abstract
Most regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically interacting elements such as enhancers, insulators or promoters. To map these elements and interactions at a fine scale, we developed HIPPIE2 that analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify precise loci of DNA physically interacting regions (PIRs). Unlike standard genome binning approaches (e.g. 10-kb to 1-Mb bins), HIPPIE2 dynamically infers the physical locations of PIRs using the distribution of restriction sites to increase analysis precision and resolution. We applied HIPPIE2 to in situ Hi-C datasets across six human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE/Roadmap functional genomic data. HIPPIE2 detected 1042 738 distinct PIRs, with high resolution (average PIR length of 1006 bp) and high reproducibility (92.3% in GM12878). PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8 million significant PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50 608 interactions were enhancer–promoter interactions and were enriched for 33 TFs, including known DNA looping/long-range mediators. These findings demonstrate that the novel dynamic approach of HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) enables the characterization of chromatin and regulatory interactions with high resolution and reproducibility.
Gaia’s detectability of black hole–main sequence star binaries formed in open clusters
Authors: Shikauchi Minori , Kumamoto Jun , Tanikawa Ataru , Fujii Michiko S 
Published: March 2020

Abstract
Black hole–main sequence star (BH–MS) binaries are one of the targets of future data releases of the astrometric satellite Gaia. They are supposed to be formed in two main sites: a galactic field and star clusters. However, previous work has never predicted the number of BH–MS binaries originating in the latter sites. In this paper we estimate the number of BH–MS binaries formed in open clusters and detectable with Gaia based on the results of N-body simulations. By considering interstellar extinction in the Milky Way and observational constraints, we predict that ∼10 BH–MS binaries are observable. We also find that chemical abundance patterns of companion MSs will help us to identify the origin of the binaries as star clusters. Such MSs are not polluted by outflows of the BH progenitors, such as stellar winds and supernova ejecta. Chemical anomalies might be a good test to confirm the origin of binaries with relatively less massive MSs (≲5 M⊙), short orbital periods (∼1.5 yr), and higher eccentricities (e ≳0.1).
Productive performance and cost benefits of feeding wistar albino rats with processed tropical sickle pod (Senna obtusifolia) leaf meal-based diets
Authors: Augustine Clement , Khobe Dishi , Madugu Altine J , Babakiri Yahaya , Joel Isa , John Tiva , Igwebuike Joseph U , Ibrahim Asabe 
Published: March 2020

AbstractA feeding trial was conducted for 28 d to evaluate the effects of feeding albino rats with processed Senna obtusifolia leaf meal (SOLM) based diets. Five experimental diets were compounded to contain 0% and 20% each of the sun-dried, boiled, fresh fermented, boiled fermented SOLM-based diets designated as T1, T2, T3, T4, and T5, respectively. A total of 90 young albino rats with initial weight of 13.52–14.48 g were randomly allocated to the dietary treatments in a completely randomized design with three replicates of six rats each. The result of the productive performance was not significantly (P &gt; 0.05) different, except feed intake, which indicated significant (P &lt; 0.05) variation. The highest total feed intake (365.40 g) was recorded in albino rats fed the control diet (0% SOLM) and 20% boiled and fermented SOLM (334.32 g). The overall weight gain among the albino rats fed the processed SOLM-based diets were not significantly (P &gt; 0.05) different. Results on cost benefits revealed a reduction in feed cost per kilogram, cost of feed intake, and feed cost per kilogram body weight gain recorded in SOLM-based diets (T2–T5). Feed cost per kilogram was observed to reduce by 21.86, 20.79, 21.80, and 18.79 in T2–T5, respectively. It was concluded that the processed SOLM-based diets had enhanced the productive performance of albino rats. However, albino rats fed the boiled and fermented SOLM-based diet indicated better feed intake compared with the other groups of rats fed the other processed SOLM-based diets. On economic grounds, the use of processed SOLM as a feed ingredient for albino rats is cost effective because of the reduction in feed cost per kilogram of the SOLM-based diets and feed cost per kilogram body weight gain observed in albino rats fed SOLM-based diets and is, therefore, recommended for feeding albino rats.
Compression wood has a minor effect on the climate signal in tree-ring stable isotope records of montane Norway spruce
Authors: Janecka Karolina , Kaczka Ryszard J , Gärtner Holger , Harvey Jill E , Treydte Kerstin 
Published: March 2020

Abstract
Compression wood (CW) is a common tissue present in the trunk, branches and roots of mechanically stressed coniferous trees. Its main role is to increase the mechanical strength and regain the vertical orientation of a leaning stem. Compression wood is thought to influence the climate signal in different tree-ring measures. Hence trees containing CW are mostly excluded from tree-ring studies reconstructing past climate variability. There is a large gap of systematic work testing the potential effect of CW on the strength of the climate signal in different tree-ring parameters, especially stable isotope records. Here we test for the first time the effect of CW contained in montane Norway spruce (Picea abies L. Karst) on both δ13C and δ18O tree-ring cellulose records by analyzing compression and opposite wood radii from several disturbed trees together with samples from undisturbed reference trees. We selected four trees tilted by geomorphic processes that were felled by wind and four undisturbed reference trees in the Tatra Mountains, Poland. We qualitatively classified the strength of CW using wood cell anatomical characteristics (tracheid shape, cell wall thickness and presence of intercellular spaces). Then we developed tree-ring width and δ13C and δ18O chronologies from the CW radii, from the opposite radii of the tilted trees and from the reference radii. We tested the effect of CW on tree-ring cellulose δ13C and δ18O variability and on the climate signal strength. We found only minor differences in the means of δ13C and δ18O of compression (δ13C: −22.81‰, δ18O: 28.29‰), opposite (δ13C: −23.02‰; δ18O: 28.05‰) and reference (δ13C: −22.78‰; δ18O: 27.61‰) radii. The statistical relationships between climate variables, δ13C and δ18O, remained consistent among all chronologies. Our findings suggest that moderately tilted trees containing CW can be used to reconstruct past geomorphic activity and for stable isotope-based dendroclimatology.
Disentangling the effects of atmospheric CO2 and climate on intrinsic water-use efficiency in South Asian tropical moist forest trees
Authors: Rahman Mizanur , Islam Mahmuda , Gebrekirstos Aster , Bräuning Achim 
Published: March 2020

AbstractDue to the increase in atmospheric CO2 concentrations, the ratio of carbon fixed by assimilation to water lost by transpiration through stomatal conductance (intrinsic water-use efficiency, iWUE) shows a long-term increasing trend globally. However, the drivers of short-term (inter-annual) variability in iWUE of tropical trees are poorly understood. We studied the inter-annual variability in iWUE of three South Asian tropical moist forest tree species (Chukrasia tabularis A.Juss., Toona ciliata M. Roem. and Lagerstroemia speciosa L.) derived from tree-ring stable carbon isotope ratio (δ13C) in response to variations of environmental conditions. We found a significantly decreasing trend in carbon discrimination (Δ13C) and an increasing trend in iWUE in all the three species, with a species-specific long-term trend in intercellular CO2 concentration (Ci). Growing season temperatures were the main driver of inter-annual variability of iWUE in C. tabularis and L. speciosa, whereas previous year temperatures determined the iWUE variability in T. ciliata. Vapor pressure deficit was linked with iWUE only in C. tabularis. Differences in shade tolerance, tree stature and canopy position might have caused this species-specific variation in iWUE response to climate. Linear mixed effect modeling successfully simulated iWUE variability, explaining 41–51% of the total variance varying with species. Commonality analysis revealed that temperatures had a dominant influence on the inter-annual iWUE variability (64–77%) over precipitation (7–22%) and atmospheric CO2 concentration (3–6%). However, the long-term variations in iWUE were explicitly determined by the atmospheric CO2 increase (83–94%). Our results suggest that the elevated CO2 and concomitant global warming might have detrimental effects on gas exchange and other physiological processes in South Asian tropical moist forest trees.
Matched Pairs Comparison of an Enhanced Recovery Pathway Versus Conventional Management on Opioid Exposure and Pain Control in Patients Undergoing Lung Surgery
Authors: Rice David , Rodriguez-Restrepo Andrea , Mena Gabriel , Cata Juan , Thall Peter , Milton Denai , Correa Arlene , Woodard TaCharra , Antonoff Mara , Hofstetter Wayne , Roth Jack , Sepesi Boris , Swisher Stephen , Walsh Garrett , Vaporciyan Ara , Mehran Reza 
Published: March 2020

Objective:
The aim of this study was to assess the effect of an enhanced recovery after surgery (ERAS) pathway on pain and opioid use following lung resection.

Summary Background Data:
A major component ERAS pathways is opioid-sparing analgesia; however, the effect on postoperative pain and opioid use in patients undergoing lung resection is unknown.

Methods:
Following implementation of an ERAS pathway for lung resection, 123 consecutive patients were identified. Patients were propensity-matched 1:1 with a group of consecutive patients (n = 907) undergoing lung resection before ERAS. Differences regarding in-hospital opioid consumption, discharge prescribing of opioids, and postoperative pain scores were examined. Morphine milligram equivalents were separately calculated including and excluding tramadol as an opioid medication.

Results:
There were no significant differences between matched patients regarding age, sex, performance status, receipt of preoperative treatment, extent of lung resection, or operative approach. Epidural analgesia was used in 66% of controls and in none of the ERAS group (P < 0.001). The number of adjunct analgesics used postoperatively was greater in the ERAS group (median 3 vs 2, P < 0.001). There was a major reduction in morphine milligram equivalents in the ERAS group whether tramadol was included (median 14.2 vs 57.8, P < 0.001) or excluded (median 2.7 vs 57.8, P < 0.001) and regardless of surgical approach. Average daily pain scores were lower in the ERAS group (median 1.3 vs 1.8, P = 0.004); however, this difference was present only among patients undergoing thoracotomy. The proportion of patients who were prescribed discharge opioids varied whether tramadol was included (96% each group, P = 1.00) or excluded (39% vs 80%, P < 0.001) in the analysis.

Conclusions:
Implementation of an ERAS pathway was associated with effective post-operative analgesia, major reductions in in-hospital consumption of opioids, and reduced pain, compared to conventional management.
Inducible Left Ventricular Outflow Tract Obstruction in Patients Undergoing Liver Transplantation: Prevalence, Predictors, and Association With Cardiovascular Events
Authors: Cailes Benjamin , Koshy Anoop N. , Gow Paul , Weinberg Laurence , Srivastava Piyush , Testro Adam , Peverelle Matthew , Ko Jefferson , Salehi Hamid , Jones Elizabeth F. , Calafiore Paul , Farouque Omar 
Published: March 2020

Background.
Inducible left ventricular outflow tract obstruction (LVOTO) is often encountered in liver transplantation (LT) candidates during cardiac workup. While the impact of LVOTO on adverse cardiovascular hemodynamics is well reported, it is unclear whether it predisposes to perioperative cardiovascular complications.

Methods.
Consecutive patients with end-stage liver disease undergoing dobutamine stress echocardiography (DSE) were evaluated at an LT center between 2010 and 2017. Perioperative major adverse cardiovascular events (MACEs) at 30 days and all-cause death were recorded from a prospectively maintained LT database.

Results.
We evaluated 560 patients who underwent DSE during LT workup, with LVOTO identified in 24.3% (n = 136). Of these, 309 patients progressed to transplant. Patients with LVOTO demonstrated a lower peak systolic blood pressure (SBP) and an overall reduction in SBP on DSE. A total of 85 MACEs were recorded in 72 patients (23.3%) including 3 deaths, 19 cases of heart failure, 11 cardiac arrests, 8 acute coronary syndromes, and 44 arrhythmias. MACE occurred in 15/64 patients (23.4%) with LVOTO and 57/245 (23.3%) without (P = 0.92). There was an increased risk of perioperative cardiac arrest in patients with LVOTO (7.4% versus 2.4%, P = 0.04). Intraoperatively, patients with LVOTO required higher doses of vasopressors (P = 0.01) and received greater volumes of fluid (10.5 ± 8.1 versus 8.4 ± 6.4 L, P = 0.03).

Conclusions.
Patients with end-stage liver disease and LVOTO demonstrate a reduction in SBP during physiological stress that may translate to hemodynamic instability during LT. LVOTO was not associated with an increased rate of perioperative MACE or death.
Syndromic detectability of haemorrhagic fever outbreaks
Authors: Glennon Emma E. , Jephcott Freya L. , Oti Alexandra , Carlson Colin J. , Bustos Carillo Fausto A. , Hranac C. Reed , Parker Edyth , Wood James L. N. , Restif Olivier 
Published: March 2020

AbstractLate detection of emerging viral transmission allows outbreaks to spread uncontrolled, the devastating consequences of which are exemplified by recent epidemics of Ebola virus disease. Especially challenging in places with sparse healthcare, limited diagnostic capacity, and public health infrastructure, syndromes with overlapping febrile presentations easily evade early detection. There is a clear need for evidence-based and context-dependent tools to make syndromic surveillance more efficient. Using published data on symptom presentation and incidence of 21 febrile syndromes, we develop a novel algorithm for aetiological identification of case clusters and demonstrate its ability to identify outbreaks of dengue, malaria, typhoid fever, and meningococcal disease based on clinical data from past outbreaks. We then apply the same algorithm to simulated outbreaks to systematically estimate the syndromic detectability of outbreaks of all 21 syndromes. We show that while most rare haemorrhagic fevers are clinically distinct from most endemic fevers in sub-Saharan Africa, VHF detectability is limited even under conditions of perfect syndromic surveillance. Furthermore, even large clusters (20+ cases) of filoviral diseases cannot be routinely distinguished by the clinical criteria present in their case definitions alone; we show that simple syndromic case definitions are insensitive to rare fevers across most of the region. We map the estimated detectability of Ebola virus disease across sub-Saharan Africa, based on geospatially mapped estimates of malaria, dengue, and other fevers with overlapping syndromes. We demonstrate “hidden hotspots” where Ebola virus is likely to spill over from wildlife and also transmit undetected for many cases. Such places may represent both the locations of past unobserved outbreaks and potential future origins for larger epidemics. Finally, we consider the implications of these results for improved locally relevant syndromic surveillance and the consequences of syndemics and under-resourced health infrastructure for infectious disease emergence.
The SARS-CoV-2 epidemic outbreak: a review of plausible scenarios of containment and mitigation for Mexico
Authors: Acuña-Zegarra Manuel Adrian , Comas-García Andreu , Hernández-Vargas Esteban , Santana-Cibrian Mario , Velasco-Hernandez Jorge X. 
Published: March 2020

AbstractWe present here several variants of a mathematical model to explore three main issues related to SARS-CoV-2 spread in scenarios similar to those present in Mexico and elsewhere in Latin America. We explore the consequences for travel inside a given region, in this case Mexico, particularly focusing on airplane transportation but attempting to give a gross approximation to terrestrial movement since this is the main form of population movement across geographical areas in the country; then we proceed to study the effect of behavioral changes required to lower transmission by lowering the contact rate and infection probability and lastly, we explore the consequences of disease spread in a population subject to social isolation.These models are not suitable for predictive purposes although some rough predictions can be extracted from them. They are presented as a tool that can serve to explore plausible scenarios of spread and impact, effectiveness and consequences of contention and mitigation policies. Given the early stage at which the epidemic is at the date of writing in Mexico, we hope these ideas can be helpful for the understanding of the importance of isolation, social distancing and screening of the general population.Key findingsWe have estimated the parameters of the epidemic curve (growth rate, carrying capacity and dispersion) as well as a first estimate of the basic reproduction number for Mexico.We provide expected trends of epidemic outbreaks depending upon of the number of imported cases per day arriving to a large airport. We illustrate this trends with data from Mexico City airport.We provide expected trends of disease dispersal depending upon of the number of exported cases per day either by airplane or bus. We illustrate this trends with data from Mexico City.We evaluate the effect of behavioral change to reduce the contact rate and compare diverse scenarios that evaluate the timing of initial enforcement of behavior, time horizon in which to diminish the contact rate and the proportion of people under isolation.We evaluate the effect of social isolation by itself with respect to two main parameters: the starting time for the enforcement of control measures, and the learning time to achieve the desired contact rate reduction. We stress the importance of quick and direct actions to isolate and reduce contact rate simultaneously.
A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production
Authors: Bhadra Sanchita , Maranhao Andre C. , Ellington Andrew D. 
Published: March 2020

ABSTRACTGiven the scale of the ongoing COVID-19 pandemic, the need for reliable, scalable testing, and the likelihood of reagent shortages, especially in resource-poor settings, we have developed a RT-qPCR assay that relies on an alternative to conventional viral reverse transcriptases, a thermostable reverse transcriptase / DNA polymerase (RTX)1. Here we show that RTX performs comparably to the other assays sanctioned by the CDC and validated in kit format. We demonstrate two modes of RTX use – (i) dye-based RT-qPCR assays that require only RTX polymerase, and (ii) TaqMan RT-qPCR assays that use a combination of RTX and Taq DNA polymerases (as the RTX exonuclease does not degrade a TaqMan probe). We also provide straightforward recipes for the purification of this alternative reagent. We anticipate that in low resource or point-of-need settings researchers could obtain the available constructs from Addgene or our lab and begin to develop their own assays, within whatever regulatory framework exists for them.We lay out protocols for dye-based and TaqMan probe-based assays, in order to best compare with ‘gold standard’ reagents. These protocols should form the basis of further modifications that can simplify the assay to the use of overexpressing cells themselves as reagents.Developing dye-based and TaqMan probe-based RT-qPCR assays with RTX