bluuebunny/crossref_metadata_2025 huggingface dataset:
One Year Outcomes From a Prospective Multicenter Investigation Device Trial of a Novel Conformal Mesh Interbody Fusion Device
Authors: Driver Joseph , Huang Kevin T. , Krag Martin , Bydon Mohamad , Nunley Pierce , Lavoie Stephane , Lu Yi , Stone Marcus , Chi John H.
Published: September 2020

Study Design.

A prospective multicenter investigational device exempt trial is underway evaluating a novel conformable mesh interbody fusion device in subjects undergoing single-level fusion for degenerative disc disease. Patients meeting inclusion and exclusion criteria were offered enrollment. There is no comparative group in this study.

Objective.

Establish the short and long-term safety and effectiveness of a novel conformable mesh interbody fusion device in subjects undergoing single-level fusion for degenerative disc disease unresponsive to conservative care.

Summary of Background Data.

Transforaminal lumbar interbody fusion remains a critical procedure for patients with degenerative lumbar disc disease. Increasingly minimally invasive techniques have been proposed to minimize muscle dissection and tissue damage with the goal of minimizing pain and length of stay.

Methods.

One hundred two subjects were enrolled across 10 sites. Ninety nine subjects remained available for follow-up at 12-months. Physical evaluations/imaging were performed serially through 12-months. Validated assessment tools included 100 mm visual analogue scale (VAS) for pain, Oswestry Disability Index (ODI) for function, and computerized tomography scan for fusion. Independent committees were used to identify adverse events and for assessment of radiographic fusion.

Results.

Reductions in low back pain (LBP)/leg pain and improvements in functional status occur early and are maintained through 12-month follow-up. Mean VAS-LBP change from baseline to 6-weeks post-op (–46 mm) continued to improve through 12 months (–51 mm). Similar trends were observed for leg pain. Mean ODI change from baseline to 6 weeks post-op (–17) was almost doubled by 12 months (–32). Fusion rates at 12-months are high (98%). No device-related serious adverse events have occurred.

Conclusion.

12-month outcomes demonstrated excellent patient compliance and positive outcomes for pain, function, fusion, and device safety. Clinical improvements were observed by 6-weeks post-op and appear durable up to 1 year later. A novel mesh interbody device may provide an alternative means of interbody fusion that reduces connective tissue disruption.

Level of Evidence: 3
A Multidisciplinary Spine Surgical Indications Conference Leads to Alterations in Surgical Plans in a Significant Number of Cases
Authors: Benton Joshua A. , Mowrey Wenzhu B. , Ramos Rafael De La Garza , Weiss Brandon T. , Gelfand Yaroslav , Castro-Rivas Erida , Williams Lavinia , Headlam Mark , Udemba Adaobi , Gitkind Andrew I. , Krystal Jonathan D. , Cho Woojin , Kinon Merritt D. , Yassari Reza , Yanamadala Vijay
Published: September 2020

Study Design.

Case series.

Objective.

To evaluate the impact of a multidisciplinary spine surgery indications conference (MSSIC) on surgical planning for elective spine surgeries.

Summary of Background Data.

Identifying methods for pairing the proper patient with the optimal intervention is of the utmost importance for improving spine care and patient outcomes. Prior studies have evaluated the utility of multidisciplinary spine conferences for patient management, but none have evaluated the impact of a MSSIC on surgical planning and decision making.

Methods.

We implemented a mandatory weekly MSSIC with all spine surgeons at our institution. Each elective spine surgery in the upcoming week is presented. Subsequently, a group consensus decision is achieved regarding the best treatment option based on the expertise and opinions of the participating surgeons. We reviewed cases presented at the MSSIC from September 2019 to December 2019. We compared the surgeon's initial proposed surgery for a patient with the conference attendees’ consensus decision on the best treatment and measured compliance rates with the group's recommended treatment.

Results.

The conference reviewed 100 patients scheduled for elective spine surgery at our indications conference during the study period. Surgical plans were recommended for alteration in 19 cases (19%) with the proportion statistically significant from zero indicated by a binomial test (P < 0.001). The median absolute change in the invasiveness index of the altered procedures was 3 (interquartile range [IQR] 1–4). Participating surgeons complied with the group's recommendation in 96.5% of cases.

Conclusion.

In conjunction with other multidisciplinary methods, MSSICs can lead to surgical planning alterations in a significant number of cases. This could potentially result in better selection of surgical candidates and procedures for particular patients. Although long-term patient outcomes remain to be evaluated, this care model will likely play an integral role in optimizing the care spine surgeons provide patients.

Level of Evidence: 4
Comparison of intraocular lens power formulas according to axial length after myopic corneal laser refractive surgery
Authors: Whang Woong-Joo , Hoffer Kenneth J. , Kim Seon-Ju , Chung So-Hyang , Savini Giacomo
Published: September 2020

Purpose:

To assess the predictive accuracy of 4 no-history intraocular lens (IOL) power formulas in eyes with prior myopic excimer laser surgery, classified in 4 groups according to their axial length (AL), and investigate the relationship between AL and predictive accuracy.

Setting:

Seoul St. Mary's Hospital, Republic of Korea.

Design:

Retrospective case series.

Methods:

IOL power was calculated with the Barrett True-K, Haigis-L, Shammas-PL, and Triple-S formulas in 4 groups classified according to AL. Primary outcomes were the median absolute error (MedAE) and percentage of eyes with a prediction error (PE) within ±0.50 diopter (D).

Results:

This study included 107 eyes of 107 patients. The Barrett True-K had the lowest MedAE when AL was <26.0 mm (0.30 D) and between 26.0 and 28.0 mm (0.54 D); in these subgroups, it had the highest percentages with a PE within ±0.50 D (71.4% and 46.2%). For AL between 28.0 and 30.0 mm, the Triple-S method showed the lowest MedAE (0.43 D) and highest percentage with a PE within ±0.50 D (58.3%). For AL ≥30.0 mm, the Shammas-PL formula produced the lowest MedAE (0.41 D) and highest percentage with a PE within ±0.50 D (58.3%). The Barrett True-K was the only formula with a correlation between AL and PE (r = −0.219/P = .023).

Conclusions:

The predictive accuracy of no-history IOL formulas depends on the AL. The Barrett True-K had the highest accuracy when AL was < 28.0 mm and the Triple-S when it ranged from 28.0 mm to 30.0 mm, whereas the Shammas-PL was more accurate when AL was ≥30.0 mm.
Resistance profile of HIV-1 quasispecies in patients under treatment failure using single molecule, real-time sequencing
Authors: Monaco Daniela C. , Zapata Lucas , Hunter Eric , Salomon Horacio , Dilernia Dario A.
Published: September 2020

Objective:

Short-read next-generation sequencing (NGS) has been implemented to study the resistance profile of HIV as it provides a higher sensitivity than Sanger sequencing. However, short-reads only generates a consensus view of the viral population rather than a reconstruction of the viral haplotypes. In this study, we evaluated the resistance profile of HIV quasispecies in patients undergoing treatment failure using SMRT sequencing.

Design:

Whole-pol RT-PCR was performed on viral RNA extracted from plasma samples of 38 HIV-positive individuals undergoing treatment failure, and sequenced in the RSII instrument. Error correction and viral haplotype phasing was performed with the Multilayer Directed Phasing and Sequencing (MDPSeq) algorithm. Presence of resistance mutations reported by the IAS-USA in 2017 was assessed using an in-house script.

Results:

The SMRT sequencing-based test detected 131/134 resistance mutations previously detected using a Sanger sequencing-based test. However, the SMRT test also identified seven additional mutations present at an estimated frequency lower than 30%. The intra-host phylogenetic analysis showed that seven samples harbored at least one resistance variant at 20--80% frequency. The haplotype-resolved sequencing revealed viral diversification and selection of new resistance during suboptimal treatment, an overall trend toward selection and accumulation of new resistance mutations, as well as the co-existence of resistant and susceptible variants.

Conclusion:

Our results validate the SMRT sequencing-based test for detection of HIV drug resistance. In addition, this method unraveled the complex dynamic of HIV quasispecies during treatment failure, which might have several implications on clinical management.
Temporal Differential Expression of Physiomarkers Predicts Sepsis in Critically Ill Adults
Authors: Mohammed Akram , Van Wyk Franco , Chinthala Lokesh K. , Khojandi Anahita , Davis Robert L. , Coopersmith Craig M. , Kamaleswaran Rishikesan
Published: September 2020

Background:

Sepsis is a life-threatening condition with high mortality rates. Early detection and treatment are critical to improving outcomes. Our primary objective was to develop artificial intelligence capable of predicting sepsis earlier using a minimal set of streaming physiological data in real time.

Methods and Findings:

A total of 29,552 adult patients were admitted to the intensive care unit across five regional hospitals in Memphis, Tenn, over 18 months from January 2017 to July 2018. From these, 5,958 patients were selected after filtering for continuous (minute-by-minute) physiological data availability. A total of 617 (10.4%) patients were identified as sepsis cases, using the Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) criteria. Physiomarkers, a set of signal processing features, were derived from five physiological data streams including heart rate, respiratory rate, and blood pressure (systolic, diastolic, and mean), captured every minute from the bedside monitors. A support vector machine classifier was used for classification. The model accurately predicted sepsis up to a mean and 95% confidence interval of 17.4 ± 0.22 h before sepsis onset, with an average test accuracy of 83.0% (average sensitivity, specificity, and area under the receiver operating characteristics curve of 0.757, 0.902, and 0.781, respectively).

Conclusions:

This study demonstrates that salient physiomarkers derived from continuous bedside monitoring are temporally and differentially expressed in septic patients. Using this information, minimalistic artificial intelligence models can be developed to predict sepsis earlier in critically ill patients.
International Committee on Systematics of Prokaryotes: Subcommittee on the Taxonomy of Aerobic Bacteroidetes (formerly Flavobacterium and Cytophaga-like bacteria)
Authors: Bowman John P. , Bernardet Jean-Francois , Frandsen Lau Ellen
Published: September 2020

Minutes of the meeting: 15 November 2017 (Skype meeting).
Understanding the compositional changes in LB Lennox medium during growth ofEscherichia coliDH5α in a 1L bioreactor
Authors: Ng Wenfa
Published: September 2020

Compositional changes in growth medium represents dynamic interplay between cell growth, biomass formation, and energy maintenance, with concomitant decrease in nutrients and increase in secreted metabolites and metabolic byproducts. Such information is important for quantifying microbial physiological response both at the population and cellular level, with respect to understanding subtle differences in microbial growth response, as well as supporting model building efforts in metabolic engineering. With the desire to understand molecular weight changes in components of LB Lennox medium as well as broth fractions present during cultivation ofEscherichia coliDH5α (ATCC 53868) at 37 °C, 400 rpm stirring and 1 VVM aeration in a 1 L bioreactor, this study used a combination of gel filtration chromatography (GFC) and reversed phase high performance liquid chromatography (RP-HPLC) for determining changes to molecular weight of different fractions of the growth medium. Experiment results revealed the difficulty of fractionating the culture broth with RP-HPLC, where no distinct peaks of narrow retention time width were obtained. More importantly, the column used for GFC was unable to differentiate small molecular weight changes on the order of a few tens to few hundred Da through a refractive index detector. Together, GFC and RP-HPLC highlighted the difficulty of fractionating LB Lennox culture broth into different distinct fractions. Finally, the study validated the use of 194 nm as detection wavelength for visualizing the chromatogram of LB Lennox medium eluted from a C-18 reversed phase column during liquid chromatography. Collectively, GFC and RP-HPLC could not fractionate LB Lennox broth ofE. coliDH5α into distinct fractions for further analysis by identification techniques such as mass spectrometry. Given the inherent complexity of complex medium such as LB Lennox, clean separation of the medium into every component with high purity may be impossible.

Graphical abstract

Short description

Broad elution profile and lack of distinct peaks in chromatogram of LB Lennox broth at 6 hours post inoculation withEscherichia coliDH5α (ATCC 53868), after attempted fractionation by C-18 reversed phase high performance liquid chromatography (RP-HPLC), revealed that separation could not be achieved with a complex mixture such as a microbiology broth. Specifically, while the objective of understanding compositional changes to culture medium during growth presents tremendous opportunities for determining the dynamic conversion of nutrients into metabolites and byproducts, difficulty of profiling all chemical constituents in a complex broth mixture meant that current model building efforts for metabolic engineering remains primitive with respect to the consortia of metabolic reactions occurringin situat the cellular level.

Subject areas

biotechnology, biochemistry, cell biology, microbiology, analytical chemistry
Studying the Interplay Between Apolipoprotein E and Education on Cognitive Decline in Centenarians Using Bayesian Beta Regression
Authors: Xiang Qingyan , Andersen Stacy , Perls Thomas T , Sebastiani Paola
Published: September 2020

Apolipoprotein E (APOE) is an important risk factor for cognitive decline and Alzheimer’s disease in aging individuals. Among the 3 known alleles of this gene: e2, e3, and e4, the e4 allele is associated with faster cognitive decline and increased risk for Alzheimer’s and dementia, while the e2 allele has a positive effect on longevity, and possibly on preservation of cognitive function. Education also has an important effect on cognition and longevity but the interplay betweenAPOEand education is not well characterized. Previous studies of the effect ofAPOEon cognitive decline often used linear regression with the normality assumption, which may not be appropriate for analyzing bounded and skewed cognitive test scores. In this paper, we applied Bayesian beta regression to assess the association betweenAPOEalleles and cognitive decline in a cohort of centenarians with longitudinal assessment of their cognitive function. The analysis confirmed the negative association between older age and cognition and the beneficial effect of education that persists even at the extreme of human lifespan in carriers of the e3 allele. In addition, the analysis showed an association betweenAPOEand cognition that is modified by education. Surprisingly, an antagonistic interaction existed between higher education andAPOEalleles, suggesting that education may reduce both positive and negative effects of this gene.
Measuring functional connectivity with wearable MEG
Authors: Boto Elena , Hill Ryan M. , Rea Molly , Holmes Niall , Seedat Zelekha A. , Leggett James , Shah Vishal , Osborne James , Bowtell Richard , Brookes Matthew J.
Published: September 2020

Optically-pumped magnetometers (OPMs) offer the potential for a step change in magnetoencephalography (MEG) enabling wearable systems that: provide improved data quality; accommodate any subject group; allow data capture during movement and offer a reduction in costs. However, OPM-MEG is still a nascent technology and, to realise its potential, it must be shown to facilitate key neuroscientific measurements, such as the characterisation of human brain networks. Networks, and the connectivities that underlie them, have become a core area of neuroscientific investigation, and their importance is underscored by many demonstrations of their perturbation in brain disorders. Consequently, a demonstration of network measurements via OPM-MEG would be a significant step forward. Here, we aimed to show that a wearable 50-channel OPM-MEG system enables characterisation of the electrophysiological connectome. To this end, we characterise connectivity in the resting state and during a simple visuo-motor task, using both OPM-MEG and a state-of-the-art 275-channel cryogenic MEG device. Our results show that connectome matrices from OPM and cryogenic systems exhibit an extremely high degree of similarity, with correlation values >70 %. This value is not measurably different to the correlation observed between connectomes measured in different subject groups, on a single scanner. In addition, similar differences in connectivity between individuals (scanned multiple times) were observed in cryogenic and OPM-MEG data, again demonstrating the fidelity of OPM-MEG data. This demonstration shows that a nascent OPM-MEG system offers results similar to a cryogenic device, even despite having ∼5 times fewer sensors. This adds weight to the argument that OPMs will ultimately supersede cryogenic sensors for MEG measurement.
Manipulating phloem transport affects wood formation but not nonstructural carbon concentrations in an evergreen conifer
Authors: Rademacher Tim , Fonti Patrick , LeMoine James M. , Fonti Marina V. , Basler David , Chen Yizhao , Friend Andrew D. , Seyednasrollah Bijan , Eckes-Shephard Annemarie H. , Richardson Andrew D.
Published: September 2020

Wood formation is a crucial process for carbon sequestration, yet how variations in carbon supply affect wood formation and carbon dynamics in trees more generally remains poorly understood.

To better understand the role of carbon supply in wood formation, we restricted phloem transport using girdling and compression around the stem of mature white pines and monitored the effects on local wood formation and stem CO2efflux, as well as nonstructural carbon concentrations in needles, stems, and roots.

Growth and stem CO2efflux varied with location relative to treatment (i.e., above or below on the stem). We observed up to a two-fold difference in the number of tracheids formed above versus below the manipulations over the remaining growing season. In contrast, the treatments did not affect mean cell size noticeably and mean cell-wall area decreased only slightly below them. Surprisingly, nonstructural carbon pools and concentrations in the xylem, needles, and roots remained largely unchanged, although starch reserves declined and increased marginally below and above the girdle, respectively.

Our results suggest that phloem transport strongly affects cell proliferation and respiration in the cambial zone of mature white pine, but has little impact on nonstructural carbon concentrations. These findings contribute to our understanding of how wood formation is controlled.

Highlight

Restrictions in phloem transport designed to affect carbon supply, lead to changes in wood formation and stem respiration of mature white pines without substantially changing local nonstructural carbon concentrations.
Defining the Syrian hamster as a highly susceptible preclinical model for SARS-CoV-2 infection
Authors: Rosenke Kyle , Meade-White Kimberly , Letko Michael , Clancy Chad , Hansen Frederick , Liu Yanan , Okumura Atsushi , Tang-Huau Tsing-Lee , Li Rong , Saturday Greg , Feldmann Friederike , Scott Dana , Wang Zhongde , Munster Vincent , Jarvis Michael A. , Feldmann Heinz
Published: September 2020

Following emergence in late 2019, SARS-CoV-2 rapidly became pandemic and is presently responsible for millions of infections and hundreds of thousands of deaths worldwide. There is currently no approved vaccine to halt the spread of SARS-CoV-2 and only very few treatment options are available to manage COVID-19 patients. For development of preclinical countermeasures, reliable and well-characterized small animal disease models will be of paramount importance. Here we show that intranasal inoculation of SARS-CoV-2 into Syrian hamsters consistently caused moderate broncho-interstitial pneumonia, with high viral lung loads and extensive virus shedding, but animals only displayed transient mild disease. We determined the infectious dose 50 to be only five infectious particles, making the Syrian hamster a highly susceptible model for SARS-CoV-2 infection. Neither hamster age nor sex had any impact on the severity of disease or course of infection. Finally, prolonged viral persistence in interleukin 2 receptor gamma chain knockout hamsters revealed susceptibility of SARS-CoV-2 to adaptive immune control. In conclusion, the Syrian hamster is highly susceptible to SARS-CoV-2 making it a very suitable infection model for COVID-19 countermeasure development.

One Sentence Summary

The Syrian hamster is highly susceptible to SARS-CoV-2 making it an ideal infection model for COVID-19 countermeasure development.
Detecting and phasing minor single-nucleotide variants from long-read sequencing data
Authors: Feng Zhixing , Clemente Jose , Wong Brandon , Schadt Eric E.
Published: September 2020

Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, co-infection of multiple pathogens. Detecting and phasing minor variants, which is to determine whether multiple variants are from the same haplotype, play an instrumental role in deciphering cellular genetic heterogeneity, but are still difficult because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, have provided an unprecedented opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrated that iGDA can accurately reconstruct haplotypes in closely-related strains of the same species (divergence≥0.011%) from long-read metagenomic data. Our approach, therefore, presents a significant advance towards the complete deciphering of cellular genetic heterogeneity.
Base Reproduction Number of COVID-19: Statistic Analysis
Authors: Zhu Hongjun , Huang Jiangping , Liu Xin
Published: September 2020

The coronavirus disease 2019 (COVID-19) has grown up to be a pandemic within a short span of time. The quantification of COVID-19 transmissibility is desired for purposes of assessing the potential for a place to start an outbreak and the extent of transmission in the absence of control measures. It is well known that the transmissibility can be measured by reproduction number. For this reason, the large amount of research focuses on the estimations of reproduction number of COVID-19. However, these previous results are controversial and even misleading. To alleviate this problem, Liu et al advised to use averaging technique. Unfortunately, the fluctuant consequence principally arises from data error or model limitations rather than stochastic noise, where the averaging technique doesn’t work well. The most likely estimation in USA and Wuhan is about 8.21 and 7.9. However, no enough evidence demonstrates the transmissibility increase of infectious agent of COVID-19 throughout the world.
Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020
Authors: Stewart Robert , Martin Evangelia , Bakolis Ioannis , Broadbent Matthew , Byrne Nicola , Landau Sabine
Published: September 2020

This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.
An optimal control policy for COVID-19 pandemic until a vaccine deployment
Authors: Sayarshad Hamid R.
Published: September 2020

When an outbreak starts spreading, policy makers have to make decisions that affects health of their citizens and the economic. Some might induce harsh measures, such as lockdown. Following a long harsh lockdown, economical declines force policy makers to rethink reopening. But what is the most effective reopening strategy? In order to provide an effective strategy, here we propose a control strategy model. Our model assesses the trade-off between social performance and limited medical resources by determining individuals’ propensities. The proposed strategy also helps decision makers to find optimal lockdown and exit strategy for each region. Moreover, the financial loss is minimized. In addition, a study of a COVID-19 dataset for Los Angeles County is performed to validate our model and its results.
Immuno-Phenotyping of High-Grade Glioma Infiltrating Immune Cells Reveals Grade Specific Differences in Cells of Myeloid Origin
Authors: Ganesh Raksha A. , Raghavan Jayashree V. , Sonpatki Pranali , Naik Divya , Arunachalam Priyanka , Shah Darshat , Lakshmikantha Akhila , Pillai Shibu , Chandrachari Komal Prasad , Mariswamappa Kiran , Sathyanarayana L. D. , Shah Nameeta , Jhunjhunwala Siddharth
Published: September 2020

Gliomas are heavily infiltrated with immune cells of myeloid origin. Past studies have shown that high-grade gliomas have a higher proportion of alternatively activated and suppressive myeloid cells when compared to low-grade gliomas, which correlate with poor prognosis. However, the differences in immune cell phenotypes within high-grade gliomas (between grade III and IV) are relatively less explored, and a correlation of phenotypic characteristics between immune cells in the blood and high grade tumors has not been performed. Additionally, myeloid cells of granulocytic origin present in gliomas remain poorly characterized. Herein, we address these questions through phenotypic characterizations of monocytes and neutrophils present in blood and tumors of individuals with glioblastoma (GBM, grade IV) or grade III gliomas. Our data show that CD163 expressing M2 monocytes are present in greater proportions in GBM tissue when compared to grade III glioma tissue. In addition, we observe that neutrophils are highly heterogeneous among individuals with glioma, and a greater proportion of granulocytic myeloid-derived suppressor cells are present in grade III gliomas when compared to GBM. Finally, we show that the expression levels of CD86 and CD63 showed a high correlation between blood and tumor, and suggest that these may be used as possible markers for prognosis.
Contrasting effects of land cover on nesting habitat use and reproductive output for bumble bees
Authors: Pugesek Genevieve , Crone Elizabeth E.
Published: September 2020

Understanding habitat quality is central to understanding the distributions of species on the landscape, as well as to conserving and restoring at-risk species. Although it is well-known that many species require different resources throughout their life cycles, pollinator conservation efforts focus almost exclusively on forage resources.

Here, we evaluate nesting habitat for bumble bees by locating nests directly on the landscape. We compared colony density and colony reproductive output forBombus impatiens, the common eastern bumble bee, across three different land cover types (hay fields, meadows, and forests). We also recorded nest site characteristics, e.g., the position of each nest site, for allBombusnests located during surveys to tease apart species-specific patterns of habitat use.

We found thatB. impatiensnests exclusively underground in two natural land cover types, forests and meadows, but not in hay fields.B. impatiensnested at similar densities in both in meadows and forests, but colonies in forests had much higher reproductive output.

In contrast toB. impatiens, B. griseocollisfrequently nested on the surface of the ground and was almost always found in meadows.B. bimaculatisnests were primarily below ground in meadows.B. perplexisnested below ground in all three habitat types, including hay fields.

For some bumble bee species in this system, e.g.,B. griseocollisandB. bimaculatis, meadows, the habitat type with abundant forage resources, may be sufficient to maintain them throughout their life cycles. However,B. impatiensmight benefit from heterogeneous landscapes with forests and meadows. Further research would be needed to evaluate whether hay fields are high-quality nesting sites for the one species that used them,B. perplexis.

Synthesis and applications. In the past,Bombusnesting studies have been perceived as prohibitively labor-intensive. This example shows that it is possible to directly measure nesting habitat use and quality for bumble bee species. Applying these methods to more areas, especially areas where at-riskBombusspp. are abundant, is an important next step for identifying bumble bee habitat needs throughout their life cycles.
DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence
Authors: Fry Amanda L. , Webster Amy , Chitrakar Rojin , Baugh L. Ryan , Hubbard E. Jane Albert
Published: September 2020

Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. InC. elegansmutant fordaf-18, the soleC. elegansPTEN ortholog, primordial germ cells (PGCs) divide inappropriately in starvation conditions, in a TOR-dependent manner. Here, we further investigated the role ofdaf-18in maintaining PGC quiescence. We found that maternal or zygoticdaf-18is sufficient to maintain cell cycle quiescence, thatdaf-18acts in the germ line and soma, and thatdaf-18affects timing of PGC divisions in fed animals. Importantly, our results also implicatedaf-18in zygotic germline gene activation, though not in germline fate specification. However, TOR is less important to zygotic germline gene expression, suggesting that in the absence of fooddaf-18/PTEN prevents inappropriate germline zygotic gene activation and cell division by distinct mechanisms.
Comparative Parallel Multi-Omics Analysis During the Induction of Pluripotent and Trophectoderm States
Authors: Jaber Mohammad , Radwan Ahmed , Loyfer Netanel , Abdeen Mufeed , Sebban Shulamit , Kolb Thorsten , Zapatka Marc , Makedonski Kirill , Ernst Aurelie , Kaplan Tommy , Buganim Yosef
Published: September 2020

Following fertilization, totipotent cells divide to generate two compartments in the early embryo: the inner cell mass (ICM) and trophectoderm (TE). It is only at the 32-64 -cell stage when a clear segregation between the two cell-types is observed, suggesting a ‘T’-shaped model of specification. Here, we examine whether the acquisition of these two statesin vitroby nuclear reprogramming share similar dynamics/trajectories. We conducted a comparative parallel multi-omics analysis on cells undergoing reprogramming to Induced pluripotent stem cells (iPSCs) and induced trophoblast stem cells (TSCs), and examined their transcriptome, methylome, chromatin accessibility and activity and genomic stability. Our analysis revealed that cells undergoing reprogramming to pluripotency and TSC state exhibit specific trajectories from the onset of the process, suggesting ‘V’-shaped model. Using these analyses, not only we could describe in detail the various trajectories toward the two states, we also identified previously unknown stage-specific reprogramming markers as well as markers for faithful reprogramming and reprogramming blockers. Finally, we show that while the acquisition of the TSC state involves the silencing of embryonic programs by DNA methylation, during the acquisition of pluripotency these specific regions are initially open but then retain inactive by the elimination of the histone mark, H3K27ac.
IL-1R1 dependent signals improve clearance of cytosolic virulent mycobacteriain vivo
Authors: van der Niet Sanne , van Zon Maaike , de Punder Karin , Grootemaat Anita , Rutten Sofie , Moorlag Simone J.C.F.M. , Houben Diane , van der Sar Astrid , Bitter Wilbert , Brosch Roland , Pando Rogelio Hernandez , Pena Maria T. , Peters Peter J. , Reits Eric A. , Mayer-Barber Katrin D. , van der Wel Nicole N.
Published: September 2020

Mycobacterium tuberculosisinfections claim more than a million lives each year and better treatments or vaccines are required. A crucial pathogenicity factor is translocation from the phago-lysosomes to the cytosol upon phagocytosis by macrophages. The translocation from the phago-lysosome into the cytosol is an ESX-1 dependent process as previously shownin vitro. Here we show thatin vivo, mycobacteria also translocate to the cytosol but mainly when host immunity is compromised. We observed only low numbers of cytosolic bacilli in mice, armadillo, zebrafish and patient material infected withM. tuberculosis, M. marinumorM. leprae. In contrast, when innate or adaptive immunity was compromised, as in SCID or IL-1R1 deficient mice, a significant number of cytosolicM. tuberculosisbacilli were detected in lungs of infected mice. Taken together,M. tuberculosisinfection is controlled by adaptive immune responses as well as IL-1R1-mediated signals that result in clearance of cells containing cytosolic mycobacteriain vivo.

Importance

For decades,Mycobacterium tuberculosisis one of the deathliest pathogens known. Despite infecting approximately one third of the human population, no effective treatment or vaccine is available. A crucial pathogenicity factor is the subcellular localization, asM. tuberculosiscan translocate from the phago-lysosome to the cytosol in macrophages. The situationin vivois more complicated. In this study we establish that high level cytosolic escape of mycobacteria can indeed occurin vivo, but mainly when host resistance is compromised. The IL-1 pathway is crucial for the control of the number of cytosolic mycobacteria. The establishment that immune signals result in clearance of cells containing cytosolic mycobacteria, connects two important fields: cell-biology and immunology which is vital for the understanding of the pathology ofM. tuberculosis.
Characterization of a late blight resistance gene homologous toR2in potato variety Payette Russet
Authors: Karki Hari S. , Halterman Dennis A. , Endelman Jeffrey B.
Published: September 2020

Breeding for late blight resistance has traditionally relied on phenotypic selection, but as the number of characterized resistance (R) genes has grown, so have the possibilities for genotypic selection. One challenge for breeding russet varieties is the lack of information about the genetic basis of resistance in this germplasm group. Based on observations of strong resistance by ‘Payette Russet’ to genotype US-23 of the late blight pathogenPhytophthora infestansin inoculated experiments, we deduced the variety must contain at least one major R gene. To identify the gene(s), 79 F1 progeny were screened using a detached leaf assay and classified as resistant vs. susceptible. Linkage mapping using markers from the potato SNP array revealed a single resistant haplotype on the short arm of chromosome group 4, which coincides with theR2/Rpi-abpt/Rpi-blb3locus. PCR amplification and sequencing of the gene in Payette revealed it is homologous toR2, and transient expression experiments inNicotiana benthamianaconfirmed its recognition of theAvr2effector. Sequencing of a small diversity panel revealed a SNP unique to resistant haplotypes at theR2locus, which was converted to a KASP marker that showed perfect prediction accuracy in the F1 population and diversity panel. Although many genotypes ofP. infestansare virulent againstR2, even when defeated this gene may be valuable as one component of a multi-genic approach to quantitative resistance.
Tissue topography steers migrating Drosophila border cells
Authors: Dai Wei , Guo Xiaoran , Cao Yuansheng , Mondo James A. , Campanale Joseph P. , Montell Brandon J. , Burrous Haley , Streichan Sebastian , Gov Nir , Rappel Wouter Jan , Montell Denise J.
Published: September 2020

Moving cells can sense and respond to physical features of the microenvironment, howeverin vivothe significance of tissue topography is mostly unknown. Here we use the Drosophila border cells, an established model forin vivocell migration, to study how chemical and physical information influence migration path selection. Live imaging, genetics, modeling, and simulations show that, although chemical cues were thought to be sufficient, microtopography is also important. Chemoattractants promote predominantly posterior movement, whereas tissue architecture presents orthogonal information, a path of least resistance concentrated near the center of the egg chamber. E-cadherin supplies a permissive haptotactic cue. Our results provide insight into how cells integrate and prioritize topographical, adhesive, and chemoattractant cues to choose one path amongst many.
Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer
Authors: Zamir Amos , Li Guanyu , Chase Katelyn , Moskovitch Robert , Sun Bo , Zaritsky Assaf
Published: September 2020

We quantitatively characterize how noisy and heterogeneous behaviors of individual cells are integrated across a population toward multicellular synchronization by studying the calcium dynamics in mechanically stimulated monolayers of endothelial cells. We used information-theory to quantify the asymmetric information-transfer between pairs of cells and define quantitative measures of how single cells receive or transmit information in the multicellular network. We find that cells take different roles in intercellular information-transfer and that this heterogeneity is associated with synchronization. Cells tended to maintain their roles between consecutive cycles of mechanical stimuli and reinforced them over time, suggesting the existence of a cellular “memory” in intercellular information transfer. Interestingly, we identified a subpopulation of cells characterized by higher probability of both receiving and transmitting information. These “communication hub” roles were stable - once a cell switched to a “communication hub” role it was less probable to switch to other roles. This stableness property of the cells led to gradual enrichment of communication hubs that was associated with the establishment of synchronization. Our analysis demonstrated that multicellular synchronization was established by effective information spread from the (local) single cell to the (global) group scale in the multicellular network. Altogether, we suggest that multicellular synchronization is driven by single cell communication properties, including heterogeneity, functional memory and information flow.
Looking at local classical and quantum forces in stable crystals using multipole-model refined electron densities and orbital-free DFT approximations
Authors: Gatti Carlo
Published: September 2020

Two distinct approaches, that ofenergyand that offorce, are adopted in quantum mechanics to get insights on chemical processes. In the second one, the net forces acting on the electrons and nuclei in a system (Ehrnefest and Hellmann–Feynman forces, respectively) are determined and alocalversion of the approach, in terms of force density fields rather than forces, has also been proposed for electrons. This is the path followed by Tsirelson & Stash (2020) in this issue ofActa Crystallographica Section B, to study for the first time the spatial distribution of the electronic forces of different nature acting in stable crystals. Interestingly, by relying on approximations taken from orbital-free DFT, all components of the inner-crystal force can be easily retrieved from multipole-model refined experimental electron densities and their derivatives. No less important is that these calculations are becoming easily doable for any X-ray density crystallographer thanks to a new version of the computer programWinXPRO, purposely developed in the study which is discussed in this commentary.
Microfinance and domestic violence
Authors: Aktaruzzaman Khondker , Farooq Omar
Published: September 2020

Purpose

The purpose of this paper is to document the impact of participation in microfinance programs on domestic violence against women.

Design/methodology/approach

This paper uses the survey data from 69 villages in Bangladesh and the instrumental variable approach to estimate the effect of participation in microcredit programs on domestic violence.

Findings

The results show that women’s participation in microcredit programs does not reduce domestic violence. However, this result is possible only when the authors do not distinguish between female borrowers who have control over credit and those who do not have control over credit. Classifying female borrowers into these two categories can significantly change the results. The authors report significantly lower physical violence against those female who have control over credit. In case of psychological violence, the authors report no significant impact of control over microcredit.

Originality/value

The novelty of the paper lies in distinguishing between physical and psychological violence.
Dosimetric evaluation of methyl red radiochromic film for radiation processing
Authors: AL Zahrany Awad , Rabaeh Khalid , Eyadeh Molham , Basfar Ahmed
Published: September 2020

Purpose

The purpose of this paper is to present a radiochromic film dosimeter containing polyvinyl alcohol (PVA) matrix and various concentrations of methyl red (MR) dye for high dose measurements.

Design/methodology/approach

The MR-PVA films were exposed to irradiation up to 60 kGy using 60Co source of gamma ray. The ultraviolet and visible regions (UV/VIS) spectrophotometry were used to examine the optical density of pre-and post-irradiated dosimeters at 424 nm.

Findings

The dose sensitivity of MR-PVA films increases significantly with increasing MR dye concentrations in the dose range of 5 to 60 kGy. The impact of relative humidity, irradiation temperature, dose rate and the stability of the films has been analyzed. The overall uncertainty of the MR-PVA film dosimeter is 6.12% (Double Standard-deviation, 95% confidence level).

Practical implications

It was found that the MR-PVA films may be used as high dose dosimeter with an acceptable overall uncertainty in routine industrial radiation processing.

Originality/value

The color bleaching of irradiated MR-PVA films in terms of specific absorbance curves increases significantly with increasing absorbed dose up to 60 kGy.
Artificial agri‐environment scheme ponds do not replicate natural environments despite higher aquatic and terrestrial invertebrate richness and abundance
Authors: Reyne Marina , Nolan Myles , McGuiggan Henry , Aubry Aurélie , Emmerson Mark , Marnell Ferdia , Reid Neil
Published: September 2020

Farmland ponds are a highly threatened freshwater habitat which has undergone dramatic losses during the last 200 years due to land drainage schemes and agricultural intensification. Agri‐environment schemes (AES) incentivize farmers to adopt farming methods to benefit biodiversity, yet there are a paucity of data evaluating the success of artificially created AES ponds as analogues of natural ponds in an attempt to recreate lost environments.

We examined variation in environmental parameters and aquatic and terrestrial invertebrate communities between 38 natural ponds and 91 artificial ponds that were created in south‐west Ireland (n = 129).

Artificial ponds in agricultural grassland did not replicate natural ponds in adjacent semi‐natural habitats differing significantly in size, pH, conductivity, productivity (indicated by submerged and emergent plant cover including algae) and surrounding vegetation structure that is, sward height. These differences significantly influenced aquatic and terrestrial invertebrate community structure with a suite of indicator taxa in both natural and artificial ponds.

The conservation value of artificial ponds in agricultural grasslands should not be underestimated as they had 43% higher aquatic species richness and 33% higher aquatic species abundance than natural ponds in adjacent semi‐natural habitats.

Synthesis and applications. We demonstrate that artificial agri‐environment scheme ponds created in agricultural grasslands, whilst not direct analogues of natural ponds in adjacent semi‐natural habitats, do fulfil a role in preserving high local biodiversity albeit representing a different community of species. Creation of ponds in farmland as well as in adjacent natural habitats could provide a wider range of environmental conditions and richer associated macroinvertebrate communities, increasing landscape connectivity and further enhancing regional biodiversity.
Azaphilones biosynthesis complements the defence mechanism of Trichoderma guizhouense against oxidative stress
Authors: Pang Guan , Sun Tingting , Yu Zhenzhong , Yuan Tao , Liu Wei , Zhu Hong , Gao Qi , Yang Dongqing , Kubicek Christian P. , Zhang Jian , Shen Qirong
Published: September 2020

Filamentous fungi are known as producers of a large array of diverse secondary metabolites (SMs) that aid in securing their environmental niche. Here, we demonstrated that the SMs have an additional role in fungal defence against other fungi: Trichoderma guizhouense, a mycoparasite, is able to antagonize Fusarium oxysporum f. sp. cubense race 4 (Foc4) by forming aerial hyphae that kill the host with hydrogen peroxide. At the same time, a gene cluster comprising two polyketide synthases is strongly expressed. Using functional genetics, we characterized this cluster and identified its products as azaphilones (termed as trigazaphilones). The trigazaphilones were found lacking of antifungal toxicity but exhibited high radical scavenging activities. The antioxidant property of trigazaphilones was in vivo functional under various tested conditions of oxidative stress. Thus, we conclude that the biosynthesis of trigazaphilones serves as a complementary antioxidant mechanism and defends T. guizhouense against the hydrogen peroxide that it produces to combat other fungi like Foc4.