bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of homozygous and hemizygous complete or partial exon deletions by whole-exome sequencing
Authors: Bigio Benedetta , Seeleuthner Yoann , Kerner Gaspard , Migaud Mélanie , Rosain Jérémie , Boisson Bertrand , Nasca Carla , Puel Anne , Bustamante Jacinta , Casanova Jean-Laurent , Abel Laurent , Cobat Aurelie 
Published: May 2021

Abstract
The detection of copy number variations (CNVs) in whole-exome sequencing (WES) data is important, as CNVs may underlie a number of human genetic disorders. The recently developed HMZDelFinder algorithm can detect rare homozygous and hemizygous (HMZ) deletions in WES data more effectively than other widely used tools. Here, we present HMZDelFinder_opt, an approach that outperforms HMZDelFinder for the detection of HMZ deletions, including partial exon deletions in particular, in WES data from laboratory patient collections that were generated over time in different experimental conditions. We show that using an optimized reference control set of WES data, based on a PCA-derived Euclidean distance for coverage, strongly improves the detection of HMZ complete exon deletions both in real patients carrying validated disease-causing deletions and in simulated data. Furthermore, we develop a sliding window approach enabling HMZDelFinder_opt to identify HMZ partial deletions of exons that are undiscovered by HMZDelFinder. HMZDelFinder_opt is a timely and powerful approach for detecting HMZ deletions, particularly partial exon deletions, in WES data from inherently heterogeneous laboratory patient collections.
Hi-C analyses with GENOVA: a case study with cohesin variants
Authors: van der Weide Robin H , van den Brand Teun , Haarhuis Judith H I , Teunissen Hans , Rowland Benjamin D , de Wit Elzo 
Published: May 2021

Abstract
Conformation capture-approaches like Hi-C can elucidate chromosome structure at a genome-wide scale. Hi-C datasets are large and require specialised software. Here, we present GENOVA: a user-friendly software package to analyse and visualise chromosome conformation capture (3C) data. GENOVA is an R-package that includes the most common Hi-C analyses, such as compartment and insulation score analysis. It can create annotated heatmaps to visualise the contact frequency at a specific locus and aggregate Hi-C signal over user-specified genomic regions such as ChIP-seq data. Finally, our package supports output from the major mapping-pipelines. We demonstrate the capabilities of GENOVA by analysing Hi-C data from HAP1 cell lines in which the cohesin-subunits SA1 and SA2 were knocked out. We find that ΔSA1 cells gain intra-TAD interactions and increase compartmentalisation. ΔSA2 cells have longer loops and a less compartmentalised genome. These results suggest that cohesinSA1 forms longer loops, while cohesinSA2 plays a role in forming and maintaining intra-TAD interactions. Our data supports the model that the genome is provided structure in 3D by the counter-balancing of loop formation on one hand, and compartmentalization on the other hand. By differentially controlling loops, cohesinSA1 and cohesinSA2 therefore also affect nuclear compartmentalization. We show that GENOVA is an easy to use R-package, that allows researchers to explore Hi-C data in great detail.
Large-scale identification of protein histidine methylation in human cells
Authors: Kapell Sebastian , Jakobsson Magnus E 
Published: May 2021

Abstract
Methylation can occur on histidine, lysine and arginine residues in proteins and often serves a regulatory function. Histidine methylation has recently attracted attention through the discovery of the human histidine methyltransferase enzymes SETD3 and METTL9. There are currently no methods to enrich histidine methylated peptides for mass spectrometry analysis and large-scale studies of the modification are hitherto absent. Here, we query ultra-comprehensive human proteome datasets to generate a resource of histidine methylation sites. In HeLa cells alone, we report 299 histidine methylation sites as well as 895 lysine methylation events. We use this resource to explore the frequency, localization, targeted domains, protein types and sequence requirements of histidine methylation and benchmark all analyses to methylation events on lysine and arginine. Our results demonstrate that histidine methylation is widespread in human cells and tissues and that the modification is over-represented in regions of mono-spaced histidine repeats. We also report colocalization of the modification with functionally important phosphorylation sites and disease associated mutations to identify regions of likely regulatory and functional importance. Taken together, we here report a system level analysis of human histidine methylation and our results represent a comprehensive resource enabling targeted studies of individual histidine methylation events.
IL-7 Immunotherapy in a Nonimmunocompromised Patient With Intractable Fungal Wound Sepsis
Authors: Turnbull Isaiah R , Mazer Monty B , Hoofnagle Mark H , Kirby John P , Leonard Jennifer M , Mejia-Chew Carlos , Spec Andrej , Blood Jane , Miles Sydney M , Ransom Eric M , Potter Robert F , Gaut Joseph P , Remy Kenneth E , Hotchkiss Richard S 
Published: May 2021

Abstract
A nonimmunocompromised patient developed life-threatening soft tissue infection with Trichosporon asahii, Fusarium, and Saksenaea that progressed despite maximum antifungal therapies and aggressive debridement. Interleukin-7 immunotherapy resulted in clinical improvement, fungal clearance, reversal of lymphopenia, and improved T-cell function. Immunoadjuvant therapies to boost host immunity may be efficacious in life-threatening fungal infections.
Hoyle–Lyttleton accretion on to black hole accretion disks with super-Eddington luminosity for dusty gas
Authors: Ogata Erika , Ohsuga Ken , Yajima Hidenobu 
Published: May 2021

Abstract
We investigate the Hoyle–Lyttleton accretion of dusty gas for the case where the central source is the black hole accretion disk. By solving the equation of motion taking into account the radiation force which is attenuated by the dust absorption, we reveal the steady structure of the flow around the central object. We find that the mass accretion rate tends to increase with an increase of the optical thickness of the flow and the gas can accrete even if the disk luminosity exceeds the Eddington luminosity for the dusty gas, since the radiation force is weakened by the attenuation via the dust absorption. When the gas flows in from the direction of the rotation axis for the disk with Γ′ = 3.0, the accretion rate is about $93\%$ of the Hoyle–Lyttleton accretion rate if τHL = 3.3 and zero for τHL = 1.0, where Γ′ is the Eddington ratio for the dusty gas and τHL is the typical optical thickness of the Hoyle–Lyttleton radius. Since the radiation flux in the direction of disk plane is small, the radiation force tends not to prevent gas accretion from the direction near the disk plane. For τHL = 3.3 and Γ′ = 3.4, although the accretion is impossible in the case of Θ = 0°, the accretion rate is $28\%$ of the Hoyle–Lyttleton one in the case of Θ = 90°, where Θ is the angle between the direction the gas is coming from and the rotation axis of the disk. We also obtain relatively high accretion luminosity that is realized when the accretion rate of the disk on to the BH is consistent with that via the Hoyle–Lyttleton mechanism taking into account the effect of radiation. This implies that the intermediate-mass black holes moving in the dense dusty gas are identified as luminous objects in the infrared band.
Phosphate Suppression of Arbuscular Mycorrhizal Symbiosis Involves Gibberellic Acid Signaling
Authors: Nouri Eva , Surve Rohini , Bapaume Laure , Stumpe Michael , Chen Min , Zhang Yunmeng , Ruyter-Spira Carolien , Bouwmeester Harro , Glauser Gaëtan , Bruisson Sébastien , Reinhardt Didier 
Published: May 2021

Abstract
Most land plants entertain a mutualistic symbiosis known as arbuscular mycorrhiza with fungi (Glomeromycota) that provide them with essential mineral nutrients, in particular phosphate (Pi), and protect them from biotic and abiotic stress. Arbuscular mycorrhizal (AM) symbiosis increases plant productivity and biodiversity and is therefore relevant for both natural plant communities and crop production. However, AM fungal populations suffer from intense farming practices in agricultural soils, in particular Pi fertilization. The dilemma between natural fertilization from AM symbiosis and chemical fertilization has raised major concern and emphasizes the need to better understand the mechanisms by which Pi suppresses AM symbiosis. Here, we test the hypothesis that Pi may interfere with AM symbiosis via the phytohormone gibberellic acid (GA) in the Solanaceous model systems Petunia hybrida and Nicotiana tabacum. Indeed, we find that GA is inhibitory to AM symbiosis and that Pi may cause GA levels to increase in mycorrhizal roots. Consistent with a role of endogenous GA as an inhibitor of AM development, GA-defective N. tabacum lines expressing a GA-metabolizing enzyme (GA methyltransferase—GAMT) are colonized more quickly by the AM fungus Rhizoglomus irregulare, and exogenous Pi is less effective in inhibiting AM colonization in these lines. Systematic gene expression analysis of GA-related genes reveals a complex picture, in which GA degradation by GA2 oxidase plays a prominent role. These findings reveal potential targets for crop breeding that could reduce Pi suppression of AM symbiosis, thereby reconciling the advantages of Pi fertilization with the diverse benefits of AM symbiosis.
Rice Non-Specific Phospholipase C6 Is Involved in Mesocotyl Elongation
Authors: Yang Di , Liu Xiong , Yin Xiaoming , Dong Tian , Yu Min , Wu Yan 
Published: May 2021

Abstract
Mesocotyl elongation of rice is crucial for seedlings pushing out of deep soil. The underlying mechanisms of phospholipid signaling in mesocotyl growth of rice are elusive. Here we report that the rice non-specific phospholipase C6 (OsNPC6) is involved in mesocotyl elongation. Our results indicated that all five OsNPCs (OsNPC1, OsNPC2, OsNPC3, OsNPC4 and OsNPC6) hydrolyzed the substrate phosphatidylcholine to phosphocholine (PCho), and all of them showed plasma membrane localization. Overexpression (OE) of OsNPC6 produced plants with shorter mesocotyls compared to those of Nipponbare and npc6 mutants. Although the mesocotyl growth of npc6 mutants was not much affected without gibberellic acid (GA)3, it was obviously elongated by treatment with GA. Upon GA3 treatment, SLENDER RICE1 (SLR1), the DELLA protein of GA signaling, was drastically increased in OE plants; by contrast, the level of SLR1 was found decreased in npc6 mutants. The GA-enhanced mesocotyl elongation and the GA-impaired SLR1 level in npc6 mutants were attenuated by the supplementation of PCho. Further analysis indicated that the GA-induced expression of phospho-base N-methyltransferase 1 in npc6 mutants was significantly weakened by the addition of PCho. In summary, our results suggest that OsNPC6 is involved in mesocotyl development via modulation of PCho in rice.
Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases
Authors: Blain-Hartung Matthew , Rockwell Nathan C. , Lagarias J. Clark 
Published: May 2021

Abstract
Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves—affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.
Evaluation of anxiety, depression and sleep quality in full-time teleworkers
Authors: Afonso Pedro , Fonseca Miguel , Teodoro Tomás 
Published: May 2021

Abstract

Background
Mental health-related positive and negative aspects of telework are understudied. This study aimed to evaluate anxiety, depression and sleep quality in full-time teleworkers during lockdown imposed by the coronavirus disease 2019 (COVID-19) pandemic and explore potential relationships between these variables, sociodemographic characteristics, quality of life and perceived productivity.

Methods
A cross-sectional study was conducted on 143 full-time teleworkers. Participants were assessed for anxiety, depression and sleep quality using validated clinical instruments.

Results
This study found a high prevalence of poor sleep quality (74%, N = 106). Participants reported anxiety/depressive symptoms with the predominance of anxiety and very high levels of sleep impairment. Better sleep quality was associated with longer sleep duration and better job satisfaction, whereas the use of hypnotic medication and higher depression/anxiety scores seem to point a correlation with sleep impairment. Anxiety/depression positively correlated with worse sleep quality and negatively associated with quality of life. Male sex was negatively associated with perceived productivity.

Conclusions
A higher prevalence of poor sleep quality was found in comparison with other studies performed during the COVID-19 pandemic as well as high levels of anxiety and depression. These results highlight the relevance of considering the potential negative impact of telework on mental health.
Factors associated with work performance and mental health of healthcare workers during pandemics: a systematic review and meta-analysis
Authors: Nowrouzi-Kia Behdin , Sithamparanathan Gobika , Nadesar Nirusa , Gohar Basem , Ott Markus 
Published: May 2021

AbstractIntroduction Healthcare workers’ work performance and mental health are associated with positive mental health outcomes and directly related to increased productivity and decreased disability costs.Methods We conducted a systematic review to identify factors associated with work performance of healthcare workers during a pandemic and conducted a meta-analysis of the prevalence of mental health outcomes in this context. Primary papers were collected and analysed using the Population/Intervention/Comparison/Outcome framework and using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. To critically appraise the studies included in the review, we used the AXIS appraisal tool to assess each cross-sectional study’s quality.Results The study identified nine factors associated with the work performance and mental health of healthcare workers, including experiencing feelings of depression, anxiety, having inadequate support, experiencing occupational stress, decreased productivity, lack of workplace preparedness, financial concerns associated with changes in income and daily living, fear of transmission and burnout/fatigue.Conclusion There is a rapidly rising need to address the work performance and mental health of healthcare workers providing timely care to patients. Regular and sustained interventions, including the use of information and communication technologies such as telehealth, are warranted.
Director Appointments: It Is Who You Know
Authors: Cai Jay , Nguyen Tu , Walkling Ralph 
Published: May 2021

AbstractUsing 9,801 director appointments during 2003–2014, we document the dramatic impact of connections. Sixty-nine percent of new directors have professional ties to incumbent boards, a group representing 13$\%$ of all potential candidates. Consistent with facilitating coordination and reducing search costs, connections help boards bring in gender diversity, new skills, and new industry background. More complex firms and firms in more competitive environments tend to appoint connected directors and experience better market reactions and higher shareholder votes. Connections to incumbent CEOs, however, result in lower announcement returns and shareholder votes. We use death (merger)-induced network loss (gain) as instruments.
Influence of Enogen Feed corn and conventional yellow dent corn in pelleted or meal-based diets on finishing pig performance and carcass characteristics
Authors: Williams Hadley R , Tokach Mike D , Woodworth Jason C , DeRouchey Joel M , Goodband Robert D , Gebhardt Jordan T 
Published: May 2021

Abstract
Genetic modification of corn has enhanced the use of different corn hybrids in animal agriculture. Enogen Feed corn, developed by Syngenta Seeds (Downers Grove, IL), has potential for use in livestock diets due to increase α-amylase enzyme in the corn thus improving starch digestibility. In addition, the pelleting process also increases starch gelatinization which increases its digestibility by the pig, increasing growth rate and improving feed efficiency. Therefore, pelleting Enogen Feed corn might prove to provide a greater response in growth performance than conventional yellow dent corn. Thus, the objective of this experiment was to determine the effects of corn source and diet form on growth performance and carcass characteristics of finishing pigs. A total of 288 pigs (53.0 ± 0.5 kg) were used with eight pigs per pen and nine pens per treatment in a 72-d study. Treatments were arranged in a 2 × 2 factorial with main effects of corn source (Enogen Feed corn or conventional yellow dent corn) and diet form (meal or pellet). For overall (d 0 to 72) performance, no interactions between corn source and diet form were observed. There was a tendency (P &lt; 0.10) for slightly improved average daily gain (ADG) and gain:feed ratio (G:F) for pigs fed conventional yellow dent corn compared to those fed Enogen Feed corn. For feed form, pigs fed pelleted diets had increased (P &lt; 0.001) ADG and G:F compared to pigs fed meal diets. For carcass characteristics, pigs fed pelleted diets had increased hot carcass weight compared to pigs fed meal diets (P &lt; 0.001). In summary, feeding pelleted diets to finishing pigs increased ADG and improved feed efficiency compared to those fed meal-based diets. There were no major differences between observed corn sources or interactions between corn source and diet form on growth performance.
Different strategies lead to a common outcome: different water-deficit scenarios highlight physiological and biochemical strategies of water-deficit tolerance in diploid versus tetraploid Volkamer lemon
Authors: Khalid Muhammad Fasih , Vincent Christopher , Morillon Raphael , Anjum Muhammad Akbar , Ahmad Shakeel , Hussain Sajjad 
Published: May 2021

AbstractWater scarcity restricts citrus growth and productivity worldwide. In pot conditions, tetraploid plants tolerate water deficit more than their corresponding diploids. However, their tolerance mechanisms remain elusive. In this study, we focused on which mechanisms (i.e., hydraulic, osmotic or antioxidative) confer water-deficit tolerance to tetraploids. We exposed diploid and tetraploid Volkamer lemon rootstock (Citrus volkameriana Tan. and Pasq.) to quickly (fast) and slowly (slow) developing water-deficit conditions. We evaluated their physiological, antioxidative defense and osmotic adjustment responses, and mineral distribution to leaves and roots. Water-deficit conditions decreased the photosynthetic variables of both diploid and tetraploid plants. Moreover, the corresponding decrease was greater in diploids than tetraploids. Higher concentrations of antioxidant enzymes, osmoprotectants and antioxidant capacity were found in the leaves and roots of tetraploids than diploids under water deficit. Diploid plants showed fast response in slow water-deficit condition, but that response did not persist as the deficit intensified. Meanwhile, tetraploids had lower water loss, which slowed the onset of slow water deficit relative to diploids. This response allowed stronger photosynthesis, while antioxidant and osmoprotectant production allowed for further tolerance once desiccation began. Overall, our results concluded that Volkamer lemon tetraploid plants tolerate rapid and slow water deficit by maintaining their photosynthesis due to low conductance (stem or roots), which helps to avoid desiccation, and stronger biochemical defense machinery than their corresponding diploids.
Negotiation Training for Case Managers to Improve Older Adult Acceptance of Services
Authors: Campbell Mobola , Seltzer Anne , Ramirez-Zohfeld Vanessa , Lindquist Lee A. 
Published: May 2021

Purpose of Study:
Older adults frequently choose not to accept recommended social support services (e.g., caregiver and home therapy). Social workers/case managers (SWs/CMs) are often caught in the conflict encouraging patients to accept services, but facing resistance. As a result, older adults may experience unsafe home scenarios and hospital discharges. This research sought to examine whether business school negotiation and dispute resolution (NDR) training could ease these conflicts and potentially improve outcomes for both older adults and SWs/CMs.

Practice Settings:
Urban health care system (pilot), national case management conference (implementation).

Methodology and Sample:
Researchers tailored the NDR training, offered at graduate business schools, for SWs/CMs. Researchers then pilot tested the NDR training at an urban hospital and implemented it with a national cohort of SWs/CMs at a national case management conference. Participants completed a survey that ascertained conflicts, utility of the NDR program, real-world applicability, and future directions.

Results:
Eighty-five SW/CM participants, from 22 states, completed the NDR training and survey. Participants reported experiencing conflicts frequently in their workday. Post-NDR training, respondents were very positive about the knowledge gained from the course, specifically noting themes of learning the negotiation basics, tactics (e.g., framing), and integrative strategies (e.g., win-win/expanding to multi-issue discussions). All participants planned to use the NDR skills in the future.

Implications for Case Management Practice:
The NDR training program can provide SWs/CMs with formal strategies to facilitate older adults' acceptance of social services while balancing patient autonomy. Learning negotiating techniques can be “win-win” for both older adults' home safety and case manager well-being.