bluuebunny/crossref_metadata_2025 huggingface dataset:
A Critical Examination of Length of Stay in Autologous Breast Reconstruction: A National Surgical Quality Improvement Program Analysis
Authors: Kotha Vikas S. , Abadeer Andrew I. , Amdur Richard L. , Song David H. , Fan Kenneth L.
Published: October 2020

Background:

This study aims to use the National Surgical Quality Improvement Program database to identify factors associated with extended postoperative length of stay after breast reconstruction with free tissue transfer.

Methods:

Consecutive cases of breast reconstruction with free tissue transfer were retrieved from the National Surgical Quality Improvement Program (2005 to 2017) database using CPT code 19364. Extended length of stay (dependent variable) was defined as greater than 5 days.

Results:

Nine thousand six hundred eighty-six cases were analyzed; extended length of stay was noted in 34 percent. On regression, patient factors independently associated with extended length of stay were body mass index (OR, 1.5; 95 percent CI, 1.2 to 1.9; p < 0.001), diabetes (OR, 1.3; 95 percent CI, 1.1 to 1.6; p = 0.003), and malignancy history (OR, 1.9; 95 percent CI, 1.22 to 3.02; p = 0.005). Operation time greater than 500 minutes (OR, 3; 95 percent CI, 2.73 to 3.28; p < 0.001) and immediate postmastectomy reconstruction (OR, 1.7; 95 percent CI, 1.16 to 2.48; p < 0.001) conferred risk for extended length of stay. Bilateral free tissue transfer was not significant. Operations performed in 2017 were at lower risk (OR, 0.2; 95 percent CI, 0.06 to 0.81; p = 0.02) for extended length of stay. Reoperation is more likely following operative transfusion and bilateral free tissue transfers, but less likely following concurrent alloplasty. Given a known operation time (minutes), postoperative length of stay (days) can be calculated using the following equation: length of stay = 2.559 + 0.003 × operation time.

Conclusions:

This study characterizes the risks for extended length of stay after free tissue transfer breast reconstruction using a prospective multicenter national database. The result of this study can be used to risk-stratify patients during surgical planning to optimize perioperative decision-making.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Risk, III.
Associations Between Financial Strain and Emotional Well-Being With Physiological Responses to Acute Mental Stress
Authors: Steptoe Andrew , Emch Sadie , Hamer Mark
Published: October 2020

Objective

This study aimed to investigate associations between financial strain and emotional well-being, health, and physiological responses to acute mental stress.

Methods

Participants were 542 healthy men and women aged 53 to 76 years from the Whitehall II study divided into those who reported no (n = 316), some (n = 135), or moderate/severe (n = 91) financial strain. Emotional well-being and self-reported health were assessed at baseline and 3 years later. Laboratory mental stress testing involved assessment of blood pressure (BP), heart rate, and lipid reactivity and recovery, and plasma interleukin 6 responses to challenging behavioral tasks. Analyses adjusted for objective financial status, age, sex, socioeconomic status (SES), and marital status.

Results

Financial strain was positively associated with more depressive symptoms; lower positive affect; greater loneliness; lower optimism, self-esteem, and sense of control; and poorer self-reported physical health, mental health, and sleep (all, p < .001). Longitudinally, financial strain predicted poorer outcomes 3 years later, but associations were attenuated after baseline levels were taken into account. Financial strain was associated with reduced systolic and diastolic BP reactivity to acute stress (mean systolic BP increase = 32.34 [15.2], 28.95 [13.1], and 27.26 [15.2] mm Hg in the none, some, and moderate/severe financial strain groups), but not with heart rate, interleukin 6, or lipid responses.

Conclusions

Financial strain was correlated with a range of emotional and health-related outcomes independently of objective financial status. The diminished BP reactions to acute mental stress suggest that financial strain may contribute to dynamic chronic allostatic load.
At the Heart of Neurological Dimensionality: Cross-Nosological and Multimodal Cardiac Interoceptive Deficits
Authors: Abrevaya Sofía , Fittipaldi Sol , García Adolfo M. , Dottori Martin , Santamaria-Garcia Hernando , Birba Agustina , Yoris Adrián , Hildebrandt Malin Katharina , Salamone Paula , De la Fuente Alethia , Alarco-Martí Sofía , García-Cordero Indira , Matorrel-Caro Miguel , Pautassi Ricardo Marcos , Serrano Cecilia , Sedeño Lucas , Ibáñez Agustín
Published: October 2020

Objective

Neurological nosology, based on categorical systems, has largely ignored dimensional aspects of neurocognitive impairments. Transdiagnostic dimensional approaches of interoception (the sensing of visceral signals) may improve the descriptions of cross-pathological symptoms at behavioral, electrophysiological, and anatomical levels. Alterations of cardiac interoception (encompassing multidimensional variables such as accuracy, learning, sensibility, and awareness) and its neural correlates (electrophysiological markers, imaging-based anatomical and functional connectivity) have been proposed as critical across disparate neurological disorders. However, no study has examined the specific impact of neural (relative to autonomic) disturbances of cardiac interoception or their differential manifestations across neurological conditions.

Methods

Here, we used a computational approach to classify and evaluate which markers of cardiac interoception (behavioral, metacognitive, electrophysiological, volumetric, or functional) offer the best discrimination between neurological conditions and cardiac (hypertensive) disease (model 1), and among neurological conditions (Alzheimer’s disease, frontotemporal dementia, multiple sclerosis, and brain stroke; model 2). In total, the study comprised 52 neurological patients (mean [standard deviation] age = 55.1 [17.3] years; 37 women), 25 cardiac patients (age = 66.2 [9.1] years; 13 women), and 72 healthy controls (age = 52.65 [17.1] years; 50 women).

Results

Cardiac interoceptive outcomes successfully classified between neurological and cardiac conditions (model 1: >80% accuracy) but not among neurological conditions (model 2: 53% accuracy). Behavioral cardiac interoceptive alterations, although present in all conditions, were powerful in differentiating between neurological and cardiac diseases. However, among neurological conditions, cardiac interoceptive deficits presented more undifferentiated and unspecific disturbances across dimensions.

Conclusions

Our result suggests a diffuse pattern of interoceptive alterations across neurological conditions, highlighting their potential role as dimensional, transdiagnostic markers.
Recent release from prison — A novel risk factor for intimate partner homicide
Authors: Cirone Justin , Keskey Robert , Hampton David , Slidell Mark , Crandall Marie , Rattan Rishi , Velopulos Catherine G. , Allen Debra , Williams Brian H. , Wilson Kenneth , Zakrison Tanya L.
Published: October 2020

BACKGROUND

The United States has the highest per-capita incarceration rate and the largest prison population in the world. More than two thirds of recently incarcerated individuals will be arrested again within 3 years of release and may commit crimes as serious as homicide soon after discharge. The pattern of homicidal violence currently remains unknown for recently incarcerated homicide suspects (RIHS) and their victims.

METHODS

A retrospective analysis of the 36 states included in the 2003 to 2017 National Violent Death Reporting System was performed with a focus on RIHS and their victims. Pearson χ2 and Wilcoxon rank sum tests were used for comparison.

RESULTS

There were 249 RIHS in the database of the 14,561 homicides where suspect recent incarceration status was documented. Compared with not–recently incarcerated suspects, RIHS were more likely to be White (41% vs. 29%, p < 0.001) and male (97% vs. 91%, p < 0.001). Recently incarcerated homicide suspects more often had a known relationship with the victim (75% vs. 51%, p < 0.001), and these homicides more often occurred in the victim’s own home (43% vs. 34%, p = 0.006). Intimate partner violence was a factor in 31% of the RIHS cases (vs. 17%, p < 0.001). The homicide weapon was most likely to be a firearm (57.8%, p < 0.001). Only 6.4% of homicides were due to mental health illness. Gang violence, while more common in the RIHS group, was still only a precipitating factor in 12.0% of the homicides (vs. 7.4%, p = 0.006).

CONCLUSION

Recently incarcerated homicide suspects are more likely to kill a known person in their own home with a firearm, and these homicides are frequently categorized as intimate partner homicides. Gang violence and mental health are not frequent precipitating factors in these deaths. Additional future interventions are urgently needed to eliminate these preventable deaths by alerting previous or current intimate partners of those being discharged from the prison system.
A multicenter study on definitive surgery for isolated hip fracture within 24 hours
Authors: Ang Darwin , Anglen Jeffrey , Ziglar Michele , Armstrong John , Offner Patrick , McKenney Mark , Plurad David , Flaherty Stephen , Gonzalez Ernest , Liu Huazhi , Danish Mary , McCormack Gregory , Nash Julie , Nagy Roger , Carrick Matthew
Published: October 2020

INTRODUCTION

Isolated hip fractures (IHFs) in the elderly are high-frequency, life-altering events. Definitive surgery ≤24 hours of admission is associated with improved outcomes. An IHF process management guideline (IHF-PMG) to expedite definitive surgery ≤24 hours was developed for a multihospital network. We report on its feasibility and subsequent patient outcomes.

METHODS

This is a prospective multicenter cohort study, involving 85 levels 1, 2, 3, and 4 trauma centers. Patients with an IHF between 65 and 100 years old were studied. Four cohorts were examined: (1) hospitals that did not implement any PMG, (2) hospitals that used their own PMG, (3) hospitals that partially used the network IHF-PMG, and (4) hospitals that used the network’s IHF-PMG. Multivariable logistic regression with reliability adjustment was used to calculate the expected value of observed to expected (O/E) mortality. Statistical significance was defined as p < 0.05.

RESULTS

Data on 24,457 IHF were prospectively collected. Following implementation of the IHF-PMG, overall IHF O/E mortality ratios decreased within the hospital network, from 1.13 in 2017 to 0.87 in 2018 and 0.86 in 2019. Hospitals that developed their own IHF-PMG or used the enterprise-wide IHF-PMG had the lowest inpatient O/E mortality at 0.59 and 0.65, respectively.

CONCLUSION

Goal-directed IHF-PMG for definitive surgery ≤24 hours was implemented across a large hospital network. The IHF-PMG was associated with lower inpatient mortality.

LEVEL OF EVIDENCE

Therapeutic/ Care management, Level III.
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics
Authors: Bryan J. Shepard , Sgouralis Ioannis , Pressé Steve
Published: October 2020

Life’s fundamental processes involve multiple molecules operating in close proximity within cells. To probe the composition and kinetics of molecular clusters confined within small (diffraction-limited) regions, experiments often report on the total fluorescence intensity simultaneously emitted from labeled molecules confined to such regions. Methods exist to enumerate total fluorophore numbers (e.g., step counting by photobleaching). However, methods aimed at step counting by photobleaching cannot treat photophysical dynamics in counting nor learn their associated kinetic rates. Here we propose a method to simultaneously enumerate fluorophores and determine their individual photophysical state trajectories. As the number of active (fluorescent) molecules at any given time is unknown, we rely on Bayesian nonparametrics and use specialized Monte Carlo algorithms to derive our estimates. Our formulation is benchmarked on synthetic and real data sets. While our focus here is on photophysical dynamics (in which labels transition between active and inactive states), such dynamics can also serve as a proxy for other types of dynamics such as assembly and disassembly kinetics of clusters. Similarly, while we focus on the case where all labels are initially fluorescent, other regimes, more appropriate to photoactivated localization microscopy, where fluorophores are instantiated in a non-fluorescent state, fall within the scope of the framework. As such, we provide a complete and versatile framework for the interpretation of complex time traces arising from the simultaneous activity of up to 100 fluorophores.
Global, regional, and national estimates of target population sizes for COVID-19 vaccination
Authors: Wang Wei , Wu Qianhui , Yang Juan , Dong Kaige , Chen Xinghui , Bai Xufang , Chen Xinhua , Chen Zhiyuan , Viboud Cécile , Ajelli Marco , Yu Hongjie
Published: October 2020

Background

COVID-19 vaccine prioritization and allocation strategies that maximize health benefit through efficient use of limited resources are urgently needed. We aimed to provide global, regional, and national estimates of target population sizes for COVID-19 vaccination to inform country-specific immunization strategies on a global scale.

Methods

Based on a previous study of international allocation for pandemic COVID-19 vaccines, we classified the entire world population into eleven priority groups. Information on priority groups was derived from a multi-pronged search of official websites, media sources and academic journal articles. The sizes of different priority groups were projected for 194 countries globally.

Results

Overall, the size of COVID-19 vaccine recipient population varied markedly by goals of the vaccination program and geography. The general population aged <60 years without any underlying condition accounts for the majority of the total population (5.2 billion people, 68%), followed by 2.3 billion individuals at risk of severe disease, and 246.9 million essential workers which are critical to maintaining a functional society. Differences in the demographic structure, presence of underlying conditions, and number of essential workers led to highly variable estimates of target populations both at the WHO region and country level. In particular, Europe has the highest share of essential workers (6.8%) and the highest share of individuals with underlying conditions (37.8%), two priority categories to maintain societal functions and reduce severe burden. In contrast, Africa has the highest share of healthy adults, school-age individuals, and infants (77.6%), which are the key groups to target to reduce community transmission.

Interpretation

The sizeable distribution of target groups on a country and regional bases underlines the importance of equitable and efficient vaccine prioritization and allocation globally. The direct and indirect benefits of COVID-19 vaccination should be balanced by considering local differences in demography and health.
Seroprevalence and Risk Factors of SARS CoV-2 in Health Care Workers of Tertiary-Care Hospitals in the Province of Khyber Pakhtunkhwa, Pakistan
Authors: Haq Mohsina , Rehman Asif , Noor Muhammad , Ahmad Jawad , Ahmad Junaid , Irfan Muhammad , Anwar Saeed , Ahmad Sajjad , Amin Said , Rahim Fawad , Haq Najib Ul
Published: October 2020

Background

High number of SARS-CoV-2 infected patients has overburdened healthcare delivery system, particularly in low-income countries. In the recent past many studies from the developed countries have been published on the prevalence of SARS CoV-2 antibodies and the risk factors of COVID-19 in healthcare-workers but little is known from developing countries.

Methods

This cross-sectional study was conducted on prevalence of SARS-CoV-2 antibody and risk factors for seropositivity in HCWs in tertiary-care hospitals of Peshawar city, Khyber Pakhtunkhwa province Pakistan.

Results

The overall seroprevalence of SARS CoV-2 antibodies was 30·7% (CI, 27·8–33·6) in 1011 HCWs. Laboratory technicians had the highest seropositivity (50·0%, CI, 31·8–68·1).

Risk analysis revealed that wearing face-mask and observing social-distancing within a family could reduce the risk (OR:0·67. p<0·05) and (OR:0·73. p<0·05) while the odds of seropositivity were higher among those attending funeral and visiting local-markets (OR:1·83. p<0·05) and (OR:1·66. p<0·01). In Univariable analysis, being a nursing staff and a paramedical staff led to higher risk of seropositivity (OR:1.58. p< 0·05), (OR:1·79. p< 0·05). Fever (OR:2·36, CI, 1·52– 3·68) and loss of smell (OR:2·95, CI: 1·46–5·98) were significantly associated with increased risk of seropositivity (p<0.01). Among the seropositive HCWs, 165 (53·2%) had no symptoms at all while 145 (46·8%) had one or more symptoms.

Conclusion

The high prevalence of SARS-CoV-2 antibodies in HCWs warrants for better training and use of protective measure to reduce their risk. Early detection of asymptomatic HCWs may be of special importance because they are likely to be potential threat to others during the active phase of viremia.
The Health Effects of Climate Change: An Overview of Systematic Reviews
Authors: Rocque Rhéa , Beaudoin Caroline , Ndjaboue Ruth , Cameron Laura , Bergeron Louann Poirier , Poulin-Rheault Rose-Alice , Fallon Catherine , Tricco Andrea C. , Witteman Holly O.
Published: October 2020

Background

Although many studies have explored the health impacts of climate change, a broader overview of research is needed to guide future research and action to mitigate and adapt to the health impacts of climate change.

Methods

We conducted an overview of systematic reviews of health impacts of climate change. We systematically searched the literature using a predefined search strategy, inclusion, and exclusion criteria. We included systematic reviews that explored at least one health impact of climate change. We organized systematic reviews according to their key characteristics, including geographical regions, year of publication and authors’ affiliations. We mapped the climate effects and health outcomes being studied and synthesized major findings.

Findings

We included ninety-four systematic reviews. Most were published after 2015 and approximately one fifth contained meta-analyses. Reviews synthesized evidence about five categories of climate impacts; the two most common were meteorological and extreme weather events. Reviews covered ten health outcome categories; the three most common were 1) infectious diseases, 2) mortality, and 3) respiratory, cardiovascular, cardiopulmonary or neurological outcomes. Most reviews suggested a deleterious impact of climate change on multiple adverse health outcomes, although the majority also called for more research.

Interpretation

Overall, most systematic reviews suggest that climate change is associated with worse human health. Future research could explore the potential explanations between these associations to propose adaptation and mitigation strategies and could include psychological and broader social health impacts of climate change.

Funding

Canadian Institutes of Health Research FDN-148426
PD-L1 lncRNA splice promotes lung adenocarcinoma progression via enhancing c-Myc activity
Authors: Qu Shuang , Jiao Zichen , Lu Geng , Yao Bing , Wang Ting , Rong Weiwei , Xu Jiahan , Fan Ting , Sun Xinlei , Yang Rong , Wang Jun , Yao Yongzhong , Xu Guifang , Yan Xin , Wang Tao , Liang Hongwei , Zen Ke
Published: October 2020

Although blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the efficacy of such immune-checkpoint inhibition strategy is limited for patients with solid tumors. The mechanism underlying the limited efficacy of PD-L1 inhibitors remains unclear. Here, we show that human lung adenocarcinoma, regardless of PD-L1 protein positive or negative, all produce a long non-coding RNA isoform of PD-L1 (PD-L1-lnc) via alternative splicing, which promotes lung adenocarcinoma proliferation and metastasis. PD-L1-lnc in various lung adenocarcinoma cells is significantly upregulated by IFNγ in a manner similar to PD-L1 mRNA. Bothin vitroandin vivostudies demonstrate that PD-L1-lnc increases proliferation and invasion but decreases apoptosis of lung adenocarcinoma cells. Mechanistically, PD-L1-lnc directly binds to c-Myc and enhances c-Myc transcriptional activity downstream in lung adenocarcinoma cells. Our results provide targeting PD-L1-lnc−c-Myc axis as a novel strategy for lung cancer therapy.
AutoCoEv – a high-throughput in silico pipeline for predicting inter-protein co-evolution
Authors: Petrov Petar B. , Awoniyi Luqman O. , Šuštar Vid , Balcı M. Özge , Mattila Pieta K.
Published: October 2020

Protein-protein communications govern cellular processes via complex regulatory networks, that are still far from being understood. Thus, identifying novel interactions between proteins can significantly facilitate our comprehension of the mechanistic principles of protein functions. Co-evolution between proteins is a sign of functional communication and, as such, provides a powerful approach to search for novel direct or indirect molecular partners. However, evolutionary analysis of large arrays of proteins, in silico, is a highly time-consuming effort, which has limited the usage of this method to protein pairs or small protein groups. Here, we developed AutoCoEv, a user-friendly computational pipeline for the search of co-evolution between a large number of proteins. By driving 15 individual programs, culminating in CAPS2 as the software for detecting co-evolution, AutoCoEv achieves seamless automation and parallelization of the workflow. Importantly, we provide a patch to CAPS2 source code to strengthen its statistical output, allowing for multiple comparisons correction and enhanced analysis of the results. We apply the pipeline to inspect co-evolution among 324 proteins identified to locate at the vicinity of the lipid rafts of B lymphocytes. We successfully detected multiple strong coevolutionary relations between the proteins, predicting many novel partners and previously unidentified clusters of functionally related molecules. We conclude that AutoCoEv, available at https://github.com/mattilalab/autocoev, can be used to predict functional interactions from large datasets in a time and cost-efficient manner.
Nebulosarecovers single cell gene expression signals by kernel density estimation
Authors: Alquicira-Hernandez Jose , Powell Joseph E.
Published: October 2020

Data sparsity in single-cell experiments prevents an accurate assessment of gene expression when visualised in a low-dimensional space. Here, we introduceNebulosa, an R package that uses weighted kernel density estimation to recover signals lost through drop-out or low expression.

Availability and implementation

Nebulosacan be easily installed fromwww.github.com/powellgenomicslab/Nebulosa
Allele-specific antisense oligonucleotide therapy for dominantly inherited hearing impairment DFNA9
Authors: de Vrieze Erik , Peijnenborg Jolien , Martin Jorge Cañas , Martens Aniek , Oostrik Jaap , van der Heuvel Simone , Neveling Kornelia , Pennings Ronald , Kremer Hannie , van Wijk Erwin
Published: October 2020

The c.151C>T founder mutation inCOCHis a frequent cause of late onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutantCOCHtranscripts has high therapeutic potential. Single-Molecule Real-Time (SMRT) sequencing resulted in the identification of 11 variants with a low population-frequency (< 10%), that are specific to the c.151C>T mutantCOCHallele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to specifically induce mutantCOCHtranscript degradation when delivered to transgenic cells expressingCOCHminigenes. Sequence optimization of the AONs against the c.151C>T mutation resulted in a lead molecule that reduced the levels of mutantCOCHtranscripts by ~60% in a transgenic cell model, without affecting wildtypeCOCHtranscript levels. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in-vitro studies indicate that AONs offer a promising treatment modality for DFNA9.
New insights into large tropical tree mass and structure from direct harvest and terrestrial lidar
Authors: Burt A. , Vicari M. Boni , da Costa A. C. L. , Coughlin I. , Meir P. , Rowland L. , Disney M.
Published: October 2020

A large portion of the terrestrial vegetation carbon stock is stored in the above-ground biomass (AGB) of tropical forests, but the exact amount remains uncertain, partly due to the lack of measurements. To date, accessible peer-reviewed data are available for just 10 large tropical trees in the Amazon that have been harvested and directly measured entirely via weighing. Here, we harvested four large tropical rainforest trees (stem diameter: 0.6–1.2m, height: 30–46m, AGB: 3960–18 584 kg) in intact old-growth forest in East Amazonia, and measured above-ground green mass, moisture content and woody tissue density. We first present rare ecological insights provided by these data, including unsystematic intra-tree variations in density, with both height and radius. We also found the majority of AGB was usually found in the crown, but varied from 42–62%. We then compare non-destructive approaches for estimating the AGB of these trees, using both classical allometry, and new lidar-based methods. Terrestrial lidar point clouds were collected pre-harvest, on which we fitted cylinders to model woody structure, enabling retrieval of volume-derived AGB. Estimates from this approach were more accurate than allometric counterparts (mean tree-scale relative error: 3% vs. 15%), and error decreased when up-scaling to the cumulative AGB of the four trees (1% vs. 15%). Further, whilst allometric error increased four-fold with tree size over the diameter range, lidar error remained constant. This suggests error in these lidar-derived estimates is random and additive. Were these results transferable across forest scenes, terrestrial lidar methods would reduce uncertainty in stand-scale AGB estimates, and therefore advance our understanding of the role of tropical forests in the global carbon cycle.
Reprogramming Epiblast Stem Cells into Pre-Implantation Blastocyst Cell-like Cells
Authors: Tomoda Kiichiro , Hu Haiming , Sahara Yoshiki , Sanyal Hashimita , Takasato Minoru , Kime Cody
Published: October 2020

Recently, a new wave of synthetic embryo systems (SESs) have been established from cultured cells toward efficient and ethical embryonic development research. We recently reported our epiblast stem cell (EPISC) reprogramming SES that generates numerous blastocyst (BC)-like hemispheres (BCLH) with pluripotent and extraembryonic cell features detected microscopically. Here, we further explored the system over key time points with unprecedented single-cell RNA sequencing (scRNA-seq) analysis and revealed broad induction of the 2C-like reporterMERVLand RNA velocity diverging three major population regions with genetic expression resembling pluripotent epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE). Enrichment of those three BC-like cell fates involved key regulons, zygotic genome activation (ZGA) related genes, specific RNA splicing, and select cells meaningfully distinguished critical regulons of model cells. This analysis confirms the induction of the extraembryonic cell populations during the reprogramming and we anticipate that our unique BCLH SES and rich data may uncover new facets of cell potency, improve developmental biology, and help biomedicine advance.
Nonself-recognition-based self-incompatibility can alternatively promote or prevent introgression
Authors: Harkness Alexander , Brandvain Yaniv
Published: October 2020

1

Traditionally, we expect that self-incompatibility alleles (S-alleles), which prevent self-fertilization, should benefit from negative-frequency dependent selection and rise to high frequency when introduced to a new population through gene flow. However, the most taxonomically widespread form of self-incompatibility, the ribonuclease-based system ancestral to the core eudicots, functions through nonself-recognition, which drastically alters the process of S-allele diversification.

We analyze a model of S-allele evolution in two populations connected by migration, focusing on comparisons among the fates of S-alleles originally unique to each population and those shared among populations.

We find that both shared and unique S-alleles originating from the population with more unique S-alleles were usually fitter than S-alleles from the population with fewer. Resident S-alleles were often driven extinct and replaced by migrant S-alleles, though this outcome could be averted by pollen limitation or biased migration.

Nonself-recognition-based self-incompatibility will usually either disfavor introgression of S-alleles or result in the whole-sale replacement of S-alleles from one population with those from another.
Using neural networks to mine text and predict metabolic traits for thousands of microbes
Authors: Hackmann Timothy J.
Published: October 2020

Microbes can metabolize more chemical compounds than any other group of organisms. As a result, their metabolism is of interest to investigators across biology. Despite the interest, information on metabolism of specific microbes is hard to access. Information is buried in text of books and journals, and investigators have no easy way to extract it out. Here we investigate if neural networks can extract out this information and predict metabolic traits. For proof of concept, we predicted two traits: whether microbes carry one type of metabolism (fermentation) or produce one metabolite (acetate). We collected written descriptions of 7,021 species of bacteria and archaea from Bergey’s Manual. We read the descriptions and manually identified (labeled) which species were fermentative or produced acetate. We then trained neural networks to predict these labels. In total, we identified 2,364 species as fermentative, and 1,009 species as also producing acetate. Neural networks could predict which species were fermentative with 97.3% accuracy. Accuracy was even higher (98.6%) when predicting species also producing acetate. We used these predictions to draw phylogenetic trees of species with these traits. The resulting trees were close to the actual trees (drawn using labels). Previous counts of fermentative species are 4-fold lower than our own. For acetate-producing species, they are 100-fold lower. This undercounting confirms past difficulty in extracting metabolic traits from text. Our approach with neural networks can extract information efficiently and accurately. It paves the way for putting more metabolic traits into databases, providing easy access of information by investigators.
Biomechanical characterization of endothelial cells exposed to shear stress using acoustic force spectroscopy
Authors: Silvani Giulia , Romanov Valentin , Cox Charles D. , Martinac Boris
Published: October 2020

Characterizing mechanical properties of cells is important for understanding many cellular processes, such as cell movement, shape, and growth, as well as adaptation to changing environments. In this study, we explore mechanical properties of endothelial cells that form the biological barrier lining blood vessels, whose dysfunction leads to development of many cardiovascular disorders. Stiffness and contractile prestress of living endothelial cells were determined byAcousticForceSpectroscopy (AFS) focusing on the displacement of functionalized microspheres located at the cell-cell periphery. The specific configuration of the acoustic microfluidic channel allowed us to develop a long-term dynamic culture protocol exposing cells to laminar flow, reaching shear stresses in the physiological range (i.e. 8 dyne cm-2) within 48 hours of barrier function maturation. A staircase-like sequence of increasing force steps, ranging from 186 pN to 3.5 nN, was applied in a single measurement revealing a force-dependent apparent stiffness in the kPa range. Moreover, our results show that different degrees of stiffening, defining the elastic behavior of the cell under different experimental conditions, i.e. static and dynamic, are caused by different levels of contractile prestress in the cytoskeleton, and are modulated by shear stress-mediated junction development and stabilization at cell borders. These results demonstrate that the AFS is capable of fast and high-throughput force measurements of adherent cells under conditions mimicking their native microenvironment, and thus revealing the shear stress dependence of mechanical properties of neighbouring endothelial cells.
Consequences of Mismatch, Misalignment and Rotation of Toric Intraocular Lenses in Refractive Cataract Surgery Part 2. Avoiding Flip Flops
Authors: I Sayegh Samir
Published: October 2020

Purpose

To show current approaches for overcorrecting astigmatism and “flipping” its axis need be reconsidered in light of methods we introduce that take into account both mismatch and misalignment of the toric intraocular lens (tIOL) with respect to the astigmatism to be corrected at the time of cataract surgery.

Setting

Private Practice and Research Center. The EYE Center. Champaign, IL, USA.

Design

Formal Analytical Study

Methods

In the most common surgical situation where both mismatch and misalignment exist, we present an analysis of the point at which overcorrection and undercorrection residuals coincide, yielding a simple but powerful methodology to predict the optimal degree of overcorrection with a tIOL. The method is illustrated for tIOLs used in surgical practice.

Results

The minimum astigmatism appropriate to overcorrect with a tIOL is given by, ,where m is the midpoint threshold used by “split-the-difference” algorithms and χ is the estimate of tIOL misalignment due to all causes. Correspondingly, the maximum overcorrection, Ωmax, that should be attempted is where is the dioptric step at the corneal plane, with σ = H − B, where H = n σ is the cylinder of the overcorrecting tIOL and B = (n − 1)σ is the cylinder of the undercorrecting tIOL, both at the IOL plane, τis the toricity ratio and γ relates to the angle of misalignment χ by which can be approximated by . Ω maxfactors elegantly in the product of , the (ideal) midpoint correction for perfect alignment, by the bracketed term, representing the percent reduction of the ideal value in a realistic surgical situation with estimated misalignment χ. To illustrate: an eye of average dimensions and tIOLs from major manufacturers , with A = 2.35 D dictating n = 5. For a misalignment of 10°Ωmax≅ 0.10 D is the maximum overcorrection that should be accepted, significantly smaller than the midpoint D, recommended by many current tIOL calculators.

Conclusion

An optimal method is presented for the selection of an overcorrecting tIOL at the time of refractive cataract surgery with improvement over current tIOL calculators’ methods.
Life cycle of arabidopsis in the international space station - Growth direction of the inflorescence stems in the presence of light under microgravity
Authors: Yashiro Umi , Karahara Ichirou , Yano Sachiko , Tamaoki Daisuke , Tanigaki Fumiaki , Shimazu Toru , Masuda Daisuke , Kasahara Haruo , Kamisaka Seiichiro
Published: October 2020

In the “Space Seed” experiment performed in Kibo module of the International Space Station, growth direction of the inflorescence stem of arabidopsis was examined under space 1G, μG, and ground 1Gconditions in the presence of light. The stems grew almost upright (vertical to the surface of seedbed) under ground 1G. Although the stems were primarily upright both under space 1Gand μG, they tilted slightly. The tilting of the stems under space 1Gwas indicated to be due to tilting of the artificial gravitational acceleration vectors produced on the centrifuge. The tilting of the stems under μGwas suggested to be due to the pressure of directional airflow produced by ventilation.
Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment
Authors: Sajuthi Andrea , White Julia , Ferguson Gayle , Freed Nikki E. , Silander Olin K.
Published: October 2020

Rapid identification of bacterial pathogens and their antimicrobial resistance (AMR) profiles is critical for minimising patient morbidity and mortality. While many sequencing methods allow deep genomic and metagenomic profiling of samples, widespread use (for example atpoint-of-care settings) is impeded because substantial sequencing and computational infrastructure is required for sequencing and analysis. Here we present Bac-PULCE (Bacterial strain and antimicrobial resistance Profiling Using Long reads via CRISPR Enrichment), which combines CRISPR-cas9 based targeted sequence enrichment with long-read sequencing. We show that this method allows simultaneous bacterial strain-level identification and antimicrobial resistance profiling of single isolates or metagenomic samples with minimal sequencing throughput. In contrast to short read sequencing, long read sequencing used in Bac-PULCE enables strain-level resolution even when targeting and sequencing highly conserved genomic regions, such as 16S rRNA. We show that these long reads allow sequencing of additional AMR genes linked to the targeted region. Additionally, long reads can be used to identify which species in a metagenomic sample harbour specific AMR loci. The ability to massively multiplex crRNAs suggests that this method has the potential to substantially increase the speed and specificity of pathogen strain identification and AMR profiling, while ensuring low computational overhead.

Importance

There is a critical need for rapid and identification of bacterial strains and antibiotic resistance profiles in clinical settings. However, most current methods require both substantial laboratory infrastructure (e.g. for DNA sequencing), substantial compute infrastructure (e.g. for bioinformatic analyses), or both. Here we present a new method, Bac-PULCE, (Bacterial strain and antimicrobial resistance Profiling Using Long reads via CRISPR Enrichment), which combines CRISPR-cas9 based targeted sequence enrichment with long-read sequencing on the Oxford Nanopore platform. This allows rapid profiling of bacterial strains and antibiotic resistance genes in a sample while requiring very little laboratory or computational infrastructure.
Early-life feeding accelerates gut microbiome maturation in piglets
Authors: Choudhury R. , Middelkoop A. , Gerrits W.J.J. , Kemp B. , Bolhuis J.E. , Kleerebezem M.
Published: October 2020

Early-life microbiome perturbations have been suggested to have important effects on host development, physiology, and behaviour, which can persist throughout life. We hypothesise that early feeding (access to a pre-weaning fibrous diet) can affect gut microbiome colonisation and development in neonatal piglets. In this longitudinal study, a customised fibrous diet was provided to early-fed piglets (EF; 6 litters) starting two days after birth until weaning (28 days of age) in addition to mother’s milk, whereas control piglets (CON; 4 litters) suckled sow’s milk only. Rectal swabs were collected at multiple timepoints until six weeks of age (i.e., 2 weeks post-weaning) to investigate intestinal microbiota composition development over time using 16S rRNA gene profiling (n = 10 piglets per treatment). We observed a dynamic intestinal microbiota colonisation pattern during the pre-weaning period in both treatment groups, which rapidly stabilised within 2 weeks post-weaning. The microbial (alpha) diversity increased with age and seemed to reach a plateau in the early post-weaning time-point (day+5). The homogenous post-weaning microbiota was represented by microbial groups includingPrevotella, Roseburia, Faecalibacterium, Ruminococcus, Megasphaera, CatenibacteriumandSubdoligranulum. Remarkably, early feeding of neonatal piglets resulted in accelerated maturation of the intestinal microbiota at pre-weaning time-points, characterised by increased rate of microbial diversity and expanded colonisation of typical post-weaning associated microbial groups (mentioned above) at pre-weaning stages. The acceleration in EF piglets was illustrated by the simultaneous emergence of typical post-weaning-associated microbial groups and a more rapid decline of typical early-life/pre-weaning microbial genera. In addition, the individual eating behaviour scores of the piglets quantitatively correlated with the accelerated change of their microbiome. Overall, these findings show the importance of early-life nutritional strategies to influence the gut microbiota maturation in piglets.
Checkpoint inhibition of origin firing prevents inappropriate replication outside of S-phase
Authors: Johnson Mark C. , Can Geylani , Santos Miguel , Alexander Diana , Zegerman Philip
Published: October 2020

Across eukaryotes, checkpoints maintain the order of cell cycle events in the face of DNA damage or incomplete replication. Although a wide array of DNA lesions activates the checkpoint kinases, whether and how this response differs in different phases of the cell cycle remains poorly understood. The S-phase checkpoint for example results in the slowing of replication, which in the budding yeastSaccharomyces cerevisiaeis caused by Rad53 kinase-dependent inhibition of the initiation factors Sld3 and Dbf4. Despite this, we show here that Rad53 phosphorylates both of these substrates throughout the cell cycle at the same sites as in S-phase, suggesting roles for this pathway beyond S-phase. Indeed we show that Rad53-dependent inhibition of Sld3 and Dbf4 limits re-replication in G2/M phase, preventing inappropriate gene amplification events. In addition we show that inhibition of Sld3 and Dbf4 after DNA damage in G1 phase prevents premature replication initiation at all origins at the G1/S transition. This study redefines the scope and specificity of the ‘S-phase checkpoint’ with implications for understanding the roles of this checkpoint in the majority of cancers that lack proper cell cycle controls.
Reproductive resilience but not root architecture underpin yield improvement in maize (Zea maysL.)
Authors: Messina Carlos , Cooper Mark , McDonald Dan , Poffenbarger Hanna , Clark Randy , Salinas Andrea , Fang Yinan , Gho Carla , Tang Tom , Graham Geoff
Published: October 2020

Plants capture soil resources to produce the grains required to feed a growing population. Because plants capture water and nutrients through roots, it was proposed that changes in root systems architecture (RSA) underpin the three-fold increase in maize grain yield over the last century1,2,3,4. Within this framework, improvements in reproductive resilience due to selection are caused by increased water capture1. Here we show that both root architecture and yield have changed with decades of maize breeding, but not the water capture. Consistent with Darwinian agriculture5theory, improved reproductive resilience6,7enabled farmers increase the number of plants per unit land8,9,10, capture soil resources, and produced more dry matter and grain. Throughout the last century, selection operated to adapt roots to crowding, enabling reallocation of C from large root systems to the growing ear and the small roots of plants cultivated in high plant populations in modern agriculture.
Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium
Authors: Jain Abhiney , Gralnick Jeffrey A.
Published: October 2020

Neutrophilic Fe(II) oxidizing bacteria likeMariprofundus ferrooxydansare obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative “omics” studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the functional understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy inM. ferrooxydans, a metabolism that has been speculated but not experimentally validated. Our work suggests thatM. ferroxydanspartitions energy generation from carbon oxidation. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.
TransMPRA: A framework for assaying the role of manytrans-acting factors at many enhancers
Authors: Calderon Diego , Ellis Andria , Daza Riza M. , Martin Beth , Tome Jacob M. , Chen Wei , Chardon Florence M. , Leith Anh , Lee Choli , Trapnell Cole , Shendure Jay
Published: October 2020

Gene regulation occurs throughtrans-acting factors (e.g.transcription factors) acting oncis-regulatory elements (e.g.enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers ofcis-regulatory elements for regulatory potential, but do not identify thetrans-acting factors that mediate any observed effects. Here we describetransMPRA — a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identifytrans-acting factors that modulate the regulatory activity of specific enhancers.
The SAGA chromatin-modifying complex: the sum of its parts is greater than the whole
Authors: Soffers Jelly H.M. , Workman Jerry L.
Published: October 2020

There are many large protein complexes involved in transcription in a chromatin context. However, recent studies on the SAGA coactivator complex are generating new paradigms for how the components of these complexes function, both independently and in concert. This review highlights the initial discovery of the canonical SAGA complex 23 years ago, our evolving understanding of its modular structure and the relevance of its modular nature for its coactivator function in gene regulation.
The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation
Authors: Zeng Yang , Ren Ren , Kaur Gundeep , Hardikar Swanand , Ying Zhengzhou , Babcock Lance , Gupta Esha , Zhang Xing , Chen Taiping , Cheng Xiaodong
Published: October 2020

The de novo DNA methyltransferases Dnmt3a and Dnmt3b play crucial roles in developmental and cellular processes. Their enzymatic activities are stimulated by a regulatory protein Dnmt3L (Dnmt3-like) in vitro. However, genetic evidence indicates that Dnmt3L functions predominantly as a regulator of Dnmt3a in germ cells. How Dnmt3a and Dnmt3b activities are regulated during embryonic development and in somatic cells remains largely unknown. Here we show that Dnmt3b3, a catalytically inactive Dnmt3b isoform expressed in differentiated cells, positively regulates de novo methylation by Dnmt3a and Dnmt3b with a preference for Dnmt3b. Dnmt3b3 is equally potent as Dnmt3L in stimulating the activities of Dnmt3a2 and Dnmt3b2 in vitro. Like Dnmt3L, Dnmt3b3 forms a complex with Dnmt3a2 with a stoichiometry of 2:2. However, rescue experiments inDnmt3a/3b/3ltriple-knockout (TKO) mouse embryonic stem cells (mESCs) reveal that Dnmt3b3 prefers Dnmt3b2 over Dnmt3a2 in remethylating genomic sequences. Dnmt3a2, an active isoform that lacks the N-terminal uncharacterized region of Dnmt3a1 including a nuclear localization signal, has very low activity in TKO mESCs, indicating that an accessory protein is absolutely required for its function. Our results suggest that Dnmt3b3 and perhaps similar Dnmt3b isoforms facilitate de novo DNA methylation during embryonic development and in somatic cells.