bluuebunny/crossref_metadata_2025 huggingface dataset:
A deficiency screen of the 3rdchromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal
Authors: Ascencio Gerson , de Cruz Matthew A. , Abuel Judy , Alvardo Sydney , Arriaga Yuma , Conrad Emily , Castro Alonso , Eichelberger Katharine , Galvan Laura , Gundy Grace , Inojoza Garcia Jorge Alberto , Jimenez Alyssa , Lu Nhein Tuyet , Lugar Catharine , Marania Ronnie , Mendsaikhan Tserendavaa , Ortega Jose , Nand Natasha , Rodrigues Nicole S. , Shabazz Khayla , Tam Cynnie , Valenciano Emannuel , Hayzelden Clive , Eritano Anthony S. , Riggs Blake
Published: October 2022

The mechanism surrounding chromosome inheritance during cell division has been well documented, however, organelle inheritance during mitosis is less understood. Recently, the Endoplasmic Reticulum (ER) has been shown to reorganize during mitosis, dividing asymmetrically in proneuronal cells prior to cell fate selection, indicating a programmed mechanism of inheritance. ER asymmetric partitioning in proneural cells relies on the highly conserved ER integral membrane protein, Jagunal (Jagn). Knockdown of Jagn in the compoundDrosophilaeye displays a pleotropic rough eye phenotype in 48% of the progeny. To identify genes involved in Jagn dependent ER partitioning pathway, we performed a dominant modifier screen of the 3rdchromosome for enhancers and suppressors of this Jagn RNAi-induced rough eye phenotype. We screened through 181 deficiency lines covering the 3L and 3R chromosomes and identified 12 suppressors and 10 enhancers of the Jagn RNAi phenotype. Based on the functions of the genes covered by the deficiencies, we identified genes that displayed a suppression or enhancement of the Jagn RNAi phenotype. These include Division Abnormally Delayed (Dally), an heparan sulfate proteoglycan, the γ-secretase subunit Presenilin, and the ER resident protein Sec63. Based on our understanding of the function of these targets, there is a connection between Jagn and the Notch signaling pathway. Further studies will elucidate the role of Jagn and identified interactors within the mechanisms of ER partitioning during mitosis.
A mind-body interface alternates with effector-specific regions in motor cortex
Authors: Gordon Evan M. , Chauvin Roselyne J. , Van Andrew N. , Rajesh Aishwarya , Nielsen Ashley , Newbold Dillan J. , Lynch Charles J. , Seider Nicole A. , Krimmel Samuel R. , Scheidter Kristen M. , Monk Julia , Miller Ryland L. , Metoki Athanasia , Montez David F. , Zheng Annie , Elbau Immanuel , Madison Thomas , Nishino Tomoyuki , Myers Michael J. , Kaplan Sydney , D’Andrea Carolina Badke , Demeter Damion V. , Feigelis Matthew , Barch Deanna M. , Smyser Christopher D. , Rogers Cynthia E. , Zimmermann Jan , Botteron Kelly N. , Pruett John R. , Willie Jon T. , Brunner Peter , Shimony Joshua S. , Kay Benjamin P. , Marek Scott , Norris Scott A. , Gratton Caterina , Sylvester Chad M. , Power Jonathan D. , Liston Conor , Greene Deanna J. , Roland Jarod L. , Petersen Steven E. , Raichle Marcus E. , Laumann Timothy O. , Fair Damien A. , Dosenbach Nico U.F.
Published: October 2022

Primary motor cortex (M1) has been thought to form a continuous somatotopic homunculus extending down precentral gyrus from foot to face representations1,2. The motor homunculus has remained a textbook pillar of functional neuroanatomy, despite evidence for concentric functional zones3and maps of complex actions4. Using our highest precision functional magnetic resonance imaging (fMRI) data and methods, we discovered that the classic homunculus is interrupted by regions with sharpy distinct connectivity, structure, and function, alternating with effector-specific (foot, hand, mouth) areas. These inter-effector regions exhibit decreased cortical thickness and strong functional connectivity to each other, and to prefrontal, insular, and subcortical regions of the Cingulo-opercular network (CON), critical for executive action5and physiological control6, arousal7, and processing of errors8and pain9. This interdigitation of action control-linked and motor effector regions was independently verified in the three largest fMRI datasets. Macaque and pediatric (newborn, infant, child) precision fMRI revealed potential cross-species analogues and developmental precursors of the inter-effector system. An extensive battery of motor and action fMRI tasks documented concentric somatotopies for each effector, separated by the CON-linked inter-effector regions. The inter-effector regions lacked movement specificity and co-activated during action planning (coordination of hands and feet), and axial body movement (e.g., abdomen, eyebrows). These results, together with prior work demonstrating stimulation-evoked complex actions4and connectivity to internal organs (e.g., adrenal medulla)10, suggest that M1 is punctuated by an integrative system for implementing whole-body action plans. Thus, two parallel systems intertwine in motor cortex to form an integrate-isolate pattern: effector-specific regions (foot, hand, mouth) for isolating fine motor control, and a mind-body interface (MBI) for the integrative whole-organism coordination of goals, physiology, and body movement.
Can Harvesting Flowers Reduce the Amount of Atmospheric Carbon Dioxide? : The Case of Cherry Blossoms
Authors: Zo Hannah , Appleyard Stephen J.
Published: October 2022

Cherry blossoms are popular as street trees in East Asia, providing an attractive backdrop to urban architecture, however their fallen petals can create a waste problem. These petals are likely to contain a significant proportion of fixed carbon so it is suggested that harvesting them may be a solution to both the waste problem and a means of quenching atmospheric CO2concomitantly. This study investigated the feasibility of flower harvesting for reducing atmospheric CO2. In particular, the total carbon (TC) stored in all cherry blossoms on streets was quantified in the geographic area of South Korea and compared to various CO2emission rates or amounts quenched by other methods. Branches with flowers were collected from different locations; the TC stored in them ranged between 41.5% - 44.8% of flower dry weights, resulting a mean flower TC per a metre of branch as 0.851±0.070 gC/m. A functional relationship of the sum of the two most apical branch lengths against crown diameter was developed to obtain an estimate of total flowering branch length from the crown diameter of a typical tree on street. The product of flowering branch length and flower TC per a metre of branch indicated that TC stored in all flowers of a tree summed to 336±163 g of carbon, equivalent to 1.23±0.60 kg CO2per tree, on average. The nationwide flower TC in each spring was calculated to be 1,900±920 tonnes of CO2, equivalent to the yearly carbon capture of 176 hectares of mature pine trees and carbon emissions from 0.24 million car operations each day. As compounds from cherry blossoms can be used extensively for pharmaceutical and cosmetic products, harvesting can be cost effective. Yet, its environmental costs and disposal after component extraction need to be considered altogether in a more complete life cycle analysis of diverting this product from landfill or decomposition.
Nucleoside-driven specificity of DNA Methyltransferase
Authors: Gade Madhuri , Gardner Jasmine M. , Jain Prashant , Laurino Paola
Published: October 2022

We have studied adenosine binding specificities of two bacterial DNA methyltransferase Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While these DNA methyltransferases have similar cofactor binding pocket interactions, experimental data showed different specificity for novel cofactors ((SNM) (S-guanosyl-L-methionine (SGM), S-cytidyl-L-methionine (SCM), S-uridyl-L-methionine (SUM)). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-L-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data proves a catalytically productive methylation by M.HhaI binding pocket for all the SNM. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.

Table of Content

TOC: Methylation by DNA methyltransferase is nucleobase dependent. While M.Taq1 is specific for SAM, M.HhaI is promiscuous for other SAM analogs
Higher habitual FODMAP intake is associated with lower body mass index, lower insulin resistance and higher short-chain fatty acid-producing microbiota in people with prediabetes
Authors: Chu NHS , He J , Ling J , Leung K , Ma RCW , Lee J , Varney J , Chan JCN , Muir JG , Chow E
Published: October 2022

Aims/hypothesis

The quantity and quality of FODMAPs can alter the relative abundance of gut microbiota with metabolic consequences although similar data are lacking in people with prediabetes. We investigated associations between habitual FODMAP contents, gut microbiota and glucose/insulin responses in subjects with prediabetes.

Methods

In this prospective cross-sectional study, ninety-eight subjects with impaired glucose tolerance (IGT) (mean age: 57±7 years, 43 % men) had assessment of body composition, 6-point oral glucose tolerance tests (OGTT), Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and 3-day dietary intake. We analysed faecal samples in a sub-group of 20 subjects with IGT and 10 subjects with normal glucose tolerance by 16S rRNA microbiome analysis.

Results

Obese subjects with IGT had the lowest daily FODMAP intake compared with their non-overweight and non-obese counterparts (5.7 (3.9-7.9) vs 7.1 (5.0-11.3) vs 9.9 (4.1-22.4) g/day, p=0.024) despite having similar total daily energy intake. Total content of FODMAPs was negatively correlated with body fat. After adjustment for age and gender, total FODMAPs were negatively associated with BMI and HOMA-IR. This remained significant after adjustment for macronutrients and physical activity (p=0.032 and p=0.036 respectively). FODMAP contents were strongly associated with short-chain fatty acid (SCFA)-producing bacteria, such asLactobacillus(p=0.011),Akkermansia muciniphila(p=0.012), andBifidobacterium longum(p=0.010), the abundance of which were negatively correlated with 2-hr plasma glucose (r = -0.524, p =0.003).

Conclusion

In individuals with IGT, higher habitual FODMAP intake was associated with lower body fat and insulin resistance and increased abundance of SCFA-producing bacteria, calling for interventional studies to evaluate the effects of FODMAP intake in prediabetes.
Effects of development and parental care on Hamilton’s force of selection
Authors: Netz Christoph
Published: October 2022

The force of selection describes the sensitivity of population growth to changes in life history parameters, with a focus usually on the survival probabilities from one age class to the next. Importantly, according to Hamilton the force of selection generally decreases after the onset of reproduction, thereby providing a possible explanation for patterns of senescence. A second characteristic feature is that the force of selection remains constant up to the age of first reproduction. This latter observation, however, rests on the assumption that offspring become independent from their parents right after birth. I show here in a minimal model that if offspring are reliant on their parents, either during early embryonal development or via parental care at later stages, the force of selection on offspring survival generally increases up until the age at which offspring become independent. This provides a possible explanation for the commonly observed pattern of decreasing mortality during early ontogeny. Further, genes acting during recurrent life stages are observed to experience a heightened force of selection compared to genes that act strictly age-specifically, demonstrating the need to develop a mechanistic understanding of gene activation patterns through which to consider life history evolution.
Spectrum preserving tilings enable sparse and modular reference indexing
Authors: Fan Jason , Khan Jamshed , Pibiri Giulio Ermanno , Patro Rob
Published: October 2022

The reference indexing problem fork-mers is to pre-process a collection of reference genomic sequencesℛso that the position of all occurrences of any queriedk-mer can be rapidly identified. An efficient and scalable solution to this problem is fundamental for many tasks in bioinformatics.

In this work, we introduce thespectrum preserving tiling(SPT), a general representation ofℛthat specifies how a set oftilesrepeatedly occur tospellout the constituent reference sequences inℛ. By encoding the order and positions wheretilesoccur, SPTs enable the implementation and analysis of a general class of modular indexes. An index over an SPT decomposes the reference indexing problem fork-mers into: (1) ak-mer-to-tile mapping; and (2) a tile-to-occurrence mapping. Recently introduced work to construct and compactly indexk-mer sets can be used to efficiently implement thek-mer-to-tile mapping. However, implementing the tile-to-occurrence mapping remains prohibitively costly in terms of space. As reference collections become large, the space requirements of the tile-to-occurrence mapping dominates that of thek-mer-to-tile mapping since the former depends on the amount of total sequence while the latter depends on the number of uniquek-mers inℛ.

To address this, we introduce a class of sampling schemes for SPTs that trade off speed to reduce the size of the tile-to-reference mapping. We implement a practical index with these sampling schemes in the toolpufferfish2. When indexing over 30,000 bacterial genomes,pufferfish2reduces the size of the tile-to-occurrence mapping from 86.3GB to 34.6GB while incurring only a 3.6× slowdown when queryingk-mers from a sequenced readset.

Supplementary materials

Sections S.1 to S.8 available online athttps://doi.org/10.5281/zenodo.7504717

Availability

pufferfish2is implemented in Rust and available athttps://github.com/COMBINE-lab/pufferfish2.
Neurotrophic and immunomodulatory lanostane triterpenoids from wood-inhabiting Basidiomycota
Authors: Hassan Khadija , Kemkuignou Blondelle Matio , Kirchenwitz Marco , Wittstein Kathrin , Rascher Monique , Chepkirui Clara , Matasyoh Josphat C. , Decock Cony , Köster Reinhard , Stradal Theresia E. B. , Stadler Marc
Published: October 2022

Neurotrophins such as nerve growth factor (ngf) and brain derived neurotrophic factor (bdnf) play important roles in the central nervous system. They are potential therapeutic drugs for treatment of neurodegerative diseases including Alzheimer’s disease and Parkinson’s disease. In this study, we investigated the neurotrophic properties of triterpenes isolated from fruiting bodies ofLaetiporus sulphureusand a mycelial culture ofAntrodiasp. MUCL 56049. The structures of the isolated compounds were elucidated based on nuclear magnetic resonance (NMR) spectroscopy in combination with high-resolution Electrospray mass spectrometry (HR-ESIMS). The secondary metabolites were tested for neurotrophin (ngfandbdnf) expression levels on human astrocytoma 1321N1 cells. Neurite outgrowth activity using rat pheochromocytoma (PC-12) cells was also determined. Twelve triterpenoids were isolated, of which several potently stimulated the expression of neurotrophic factors namely,ngf(sulphurenic acid, 15α-dehydroxytrametenolic acid, fomefficinic acid D and 16α-hydroxyeburicoic acid) andbdnf(sulphurenic acid and 15α- dehydroxytrametenolic acid), respectively. The triterpenes also potentiatedngf-induced neurite outgrowth in PC-12 cells. This is, to the best of our knowledge, the first report on the compound class of lanostanes in direct relation tobdnfandngfenhancement. These compounds are widespread in medicinal mushrooms; hence, they appear promising as starting point for development of drugs and mycopharmaceuticals to combat neurodegenerative diseases. Interestingly, they do not show any pronounced cytotoxicity and may therefore be better suited for therapy than many other neurotrophic compounds that were previously reported.
Game Bird Carcasses are Less Persistent Than Raptor Carcasses, But Can Predict Raptor Persistence Dynamics
Authors: Hallingstad Eric , Riser-Espinoza Daniel , Brown Samantha , Rabie Paul , Haddock Jeanette , Kosciuch Karl
Published: October 2022

Researchers conduct post-construction fatality monitoring (PCFM) to determine a wind energy facility’s direct impacts on wildlife. Results of PCFM can be used to evaluate compliance with permitted take, potentially triggering adaptive management measures or offsetting mitigation; reducing uncertainty in fatality rates benefits wind companies, wildlife agencies, and other stakeholders. As part of PCFM, investigators conduct carcass persistence trials to account for imperfect detection during carcass surveys. In most PCFM studies, pen-raised game birds and other non-raptor surrogates have been used to estimate persistence of all large birds, including raptors. However, there is a growing body of evidence showing carcass persistence varies by bird type; raptor fatality estimates based on game bird carcass persistence may therefore be biased high. We conducted raptor and game bird carcass persistence field trials for 1 year at 6 wind energy facilities. Raptor carcass persistence varied by habitat and season, whereas the best-supported game bird model only included habitat. Raptor persistence probabilities were higher than corresponding game bird persistence probabilities for 13 of the 16 habitat and season combinations. Analysis of a meta-dataset showed that raptor carcass persistence varied by season, habitat, and region. The probability of persisting through a 30-day search interval ranged from 0.44 to 0.99 for raptors and from 0.16 to 0.79 for game birds. Raptor persistence was significantly higher than game bird persistence for 95% of the sampled strata. We used these carcass persistence estimates to develop linear mixed-effects models that predict raptor persistence probabilities based on estimated game bird persistence probabilities. Our scaling model provides an important statistical method to address gaps in raptor persistence data at sites in a broad range of landscape contexts in the continental United States and should be used to inform fatality estimation when site-specific raptor persistence data are limited or absent.
Proliferative Exhausted CD8 T Cells Exacerbate Long-lasting Anti-tumor Effects in Human Papillomavirus Positive Head and Neck Squamous Cell Carcinoma
Authors: Cheng Danni , Qiu Ke , Rao Yufang , Mao Minzi , Li Li , Wang Yan , Song Yao , Chen Junren , Yi Xiaowei , Shao Xiuli , Huang Shao Hui , Zhang Yi , Chen Xuemei , Wu Sisi , Yu Shuaishuai , Liu Jun , Wang Haiyang , Peng Xingchen , Li Daibo , Yang Lin , Chen Li , Ying Zhiye , Zheng Yongbo , Zheng Meijun , Ying Binwu , Zeng Xiaoxi , Zhang Wei , Xu Wei , Liu Geoffrey , Chen Fei , Yu Haopeng , Zhao Yu , Ren Jianjun
Published: October 2022

The survival prognosis of human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) is largely different, and little is known about the anti-tumor mechanism of tumor-infiltrated CD8+exhausted T cells (Tex) in HNSCC. We performed cell level multi-omics sequencing on human HNSCC samples to decipher the multi-dimensional characteristics of Tex cells. A proliferative exhausted CD8+T cell cluster (P-Tex) which was beneficial to survival outcomes of patients with HPV-positive HNSCC was identified. Interestingly, P-Tex cells expressed CDK4 genes as high as cancer cells, which could be simultaneously inhibited by CDK4 inhibitors and might be a potential reason for the ineffectiveness of CDK4 inhibitors in treating HPV-positive HNSCC. P-Tex cells could aggregate in the antigen presenting cell niches and activate certain signaling pathways. Together, our findings suggest a promising role for P-Tex cells in the prognosis of patients with HPV-positive HNSCC by providing modest but persistent anti-tumor effects.

Graphic abstract
Experimental Diets Dictate the Metabolic Benefits of Probiotics in Obesity
Authors: Søgaard Larsen Ida , Choi Béatrice S.-Y. , Föh Bandik , Kristensen Nanna Ny , Ouellette Adia , Haller Rune Falkenberg , Olsen Peter Bjarke , Saulnier Delphine , Sina Christian , Jensen Benjamin A. H. , Marette André
Published: October 2022

Background

Growing evidence supports the use of probiotics to prevent or mitigate obesity-related dysmetabolism and non-alcoholic fatty liver disease (NAFLD). However, frequent reports of responders versus non-responders to probiotic treatment warrant a better understanding of key modifiers of host-microbe interactions. The influence of host diet on probiotic efficacy, in particular against metabolic diseases, remains elusive.

Method

We fed C57BL6/J mice a low fat reference diet or one of two energy-matched high fat and high sucrose diets for 12 weeks; a classical high fat diet (HFD) and a customized fast food-mimicking diet (FFMD). During the studies, mice fed either obesogenic diet were gavaged daily with one of two probiotic lactic acid bacteria (LAB) strains previously classified asLactobaccillus, namelyLimosilactobacillus reuteri(L. reuteri) orLacticaseibacillus paracaseisubsp.paracasei(L. paracasei), or vehicle.

Results

The tested probiotics exhibited a reproducible efficacy but dichotomous response according to the obesogenic diets used. Indeed,L. paracaseiprevented weight gain, improved insulin sensitivity, and protected against NAFLD development in mice fed HFD, but not FFMD. Conversely,L. reuteriimproved glucoregulatory capacity, reduced NAFLD development, and increased distal gut bile acid levels associated with changes in predicted functions of the gut microbiota exclusively in the context of FFMD-feeding.

Conclusion

We found that the probiotic efficacy of two LAB strains is highly dependent on experimental obesogenic diets. These findings highlight the need to carefully consider the confounding impact of diet in order to improve both the reproducibility of preclinical probiotic studies and their clinical research translatability.

Graphical abstract
Green synthesis of ZnO nanoparticles usingCocos nuciferaleaf extract: Characterization, antimicrobial, antioxidant, and photocatalytic activity
Authors: Rahman Farjana , Patwary Md Abdul Majed , Siddique Md. Abu Bakar , Bashar Muhammad Shahriar , Haque Md. Aminul , Akter Beauty , Rashid Rimi , Haque Md. Anamul , Uddin A. K. M. Royhan
Published: October 2022

Zinc oxide nanoparticles (ZnO NPs) have been successfully prepared usingCocos nuciferaleaf extract and investigated with their antimicrobial, antioxidant, and photocatalytic activity. The structural, compositional, and morphological properties of the NPs were recorded and studied systematically to confirm the synthesis. The aqueous suspension of NPs showed a UV-Vis. absorption maxima of 370 nm indicating primarily its formation. The XRD analysis identified the NPs with hexagonal wurtzite structure with an average particle size of 16.6 nm. The FTIR analysis identified some biomolecules and functional groups in the leaf extract as responsible for the encapsulation and stabilization of ZnO NPs. The EDX analysis showed the desired elemental compositions in the material. A flower-shaped morphology of ZnO NPs was observed by SEM with a grain size of around 15 nm. The optical properties of the NPs were studied by UV-Vis spectroscopy and the band gap was calculated as 3.37 eV. The prepared ZnO NPs have demonstrated antimicrobial activity againstT. harzianum and S. aureuswith a ZOI (zone of inhibition) of 14 and 10 mm, respectively. The photocatalytic behavior of ZnO NPs showed absorbance degradation at around 640 nm and discolored methylene blue dye after one hour with a degradation maximum of 84.29 %. Thus, the prepared ZnO NPs could be used potentially in antibiotic development, pharmaceutical industries, and as photocatalysts.
Molecular basis of the pH-controlled maturation of the tick-borne encephalitis flavivirus
Authors: Bignon Emmanuelle , Dumont Elise , Monari Antonio
Published: October 2022

Flaviviruses are enveloped viruses causing high public concerns. Their maturation spans several cellular compartments having different pH. Thus, complex control mechanisms are in place to avoid premature maturation. Here we report the dynamical behavior at neutral and acidic pH of the precursor of the membrane fusion protein E of tick-borne encephalitis, showing the different stabilization of the E dimer and the role played by the small fusion-assisting protomer (pr). The comprehension, at atomic resolution, of the fine regulation of viral maturation will be fundamental to the development of efficient strategies against emerging viral threats.
HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion
Authors: Lin Julie Qiaojin , Khuperkar Deepak , Pavlou Sofia , Makarchuk Stanislaw , Patikas Nikolaos , Lee Flora C.Y. , Kang Jianning , Field Sarah F. , Zbiegly Julia M. , Freeman Joshua L. , Ule Jernej , Metzakopian Emmanouil , Ruepp Marc-David , Mallucci Giovanna R.
Published: October 2022

Enhanced expression of the cold-shock protein RNA binding motif 3 (RBM3) is highly neuroprotective bothin vitroandin vivo. Whilst upstream signalling pathways leading to RBM3 expression have been described, the precise molecular mechanism of RBM3 induction during cooling remains elusive. To identify temperature-dependent modulators of RBM3, we performed a genome-wide CRISPR-Cas9 knockout screen using RBM3-reporter human iPSC-derived neurons. We found that RBM3 mRNA and protein levels are robustly regulated by several splicing factors, with heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) being the strongest positive regulator. Splicing analysis revealed that moderate hypothermia significantly represses the inclusion of a poison exon, which, when retained, targets the mRNA for nonsense-mediated decay. Importantly, we show that HNRNPH1 mediates this cold-dependent exon skipping via its interaction with a G-rich motif within the poison exon. Our study provides novel mechanistic insights into the regulation of RBM3 and provides further targets for neuroprotective therapeutic strategies.

Graphical Abstract
Elevated estradiol during a hormone simulated pseudopregnancy decreases sleep and increases hypothalamic activation in female Syrian hamsters
Authors: Irvine Abiola , Gaffney Maeve I. , Haughee Erin K. , Horton Marité A. , Morris Hailey C. , Harris Kagan C. , Corbin Jaclyn E. , Merrill Clara , Perlis Michael L. , Been Laura E.
Published: October 2022

Sleep disruptions are a common occurrence during the peripartum period. While physical and environmental factors associated with pregnancy and newborn care account for some sleep disruptions, there is evidence that peripartum fluctuations in estrogens may independently impact sleep. We therefore used a hormone-simulated pseudopregnancy in female Syrian hamsters to test the hypothesis that pregnancy-like increases in estradiol decrease sleep in the absence of other factors. Adult female Syrian hamsters were ovariectomized and given daily hormone injections that simulate estradiol levels during early pregnancy, late pregnancy, and the postpartum period. Home cage video recordings were captured at seven timepoints and videos were analyzed for actigraphy. During “late pregnancy,” total sleep time and sleep efficiency were decreased in hormone-treated animals during the white light period compared to vehicle controls. During both “early pregnancy” and “late pregnancy,” locomotion was increased in the white light period for hormone-treated animals; this change continued into the “postpartum period” for animals who continued to receive estradiol treatment, but not for animals who were withdrawn from estradiol. At the conclusion of the experiment, animals were euthanized and cFos expression was quantified in the ventral lateral preoptic area (VLPO) and lateral hypothalamus (LH). Animals who continued to receive high levels of estradiol during the “postpartum” period had significantly more cFos in the VLPO and LH than animals who were withdrawn from hormones or vehicle controls. Together, these data suggest that increased levels of estradiol during pregnancy are associated with sleep suppression which may be mediated by increased activation of hypothalamic nuclei.
Thiovibrio frasassiensisgen. nov., sp. nov., an autotrophic, elemental sulfur disproportionating bacterium isolated from sulfidic karst sediment, and proposal of Thiovibrionaceae fam. nov.
Authors: Aronson H.S. , Thomas C. , Bhattacharyya M.K. , Eckstein S.R. , Jensen S.R. , Barco R.A. , Macalady J.L. , Amend J.P.
Published: October 2022

A novel, autotrophic, mesophilic bacterium, strain RS19-109T, was isolated from sulfidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulfur (S0) and thiosulfate, but not sulfite with bicarbonate/CO2as a carbon source. Autotrophic growth was also observed with molecular hydrogen as an electron donor, and S0, sulfate, thiosulfate, nitrate, and ferric iron as electron acceptors. Oxygen was not used as an electron acceptor and sulfide was not used as an electron donor. Weak growth was observed with sulfate as an electron acceptor and organic carbon as electron donors and carbon sources. The strain also showed weak growth by fermentation of tryptone. Strain RS19-109Twas found to be phylogenetically distinct based on 16S rRNA gene sequence similarity (89.2%) to its closest relative,Desulfurivibrio alkaliphilusAHT2T. The draft genome sequence for strain RS19-109Thad average nucleotide identity, average amino acid identity, andin silicoDNA-DNA hybridization values of 72.2%, 63.0%, and 18.3%, respectively, compared with the genome sequence ofD. alkaliphilusAHT2T. On the basis of its physiological and genomic properties, strain RS19-109Tis proposed as the type strain of a novel species of a novel genus,Thiovibrio frasassiensisgen. nov., sp. nov. A novel family,Thiovibrionaceaefam. nov., is proposed to accommodateThiovibriowithin the order Desulfobulbales.
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients
Authors: Pita-Juarez Yered , Karagkouni Dimitra , Kalavros Nikolaos , Melms Johannes C. , Niezen Sebastian , Delorey Toni M. , Essene Adam L , Brook Olga R. , Pant Deepti , Skelton-Badlani Disha , Naderi Pourya , Huang Pinzhu , Pan Liuliu , Hether Tyler , Andrews Tallulah S. , Ziegler Carly G.K. , Reeves Jason , Myloserdnyy Andriy , Chen Rachel , Nam Andy , Phelan Stefan , Liang Yan , Amin Amit Dipak , Biermann Jana , Hibshoosh Hanina , Veregge Molly , Kramer Zachary , Jacobs Christopher , Yalcin Yusuf , Phillips Devan , Slyper Michal , Subramanian Ayshwarya , Ashenberg Orr , Bloom-Ackermann Zohar , Tran Victoria M. , Gomez James , Sturm Alexander , Zhang Shuting , Fleming Stephen J. , Warren Sarah , Beechem Joseph , Hung Deborah , Babadi Mehrtash , Padera Robert F. , MacParland Sonya A. , Bader Gary D. , Imad Nasser , Solomon Isaac H. , Miller Eric , Riedel Stefan , Porter Caroline B.M. , Villani Alexandra-Chloé , Tsai Linus T.-Y. , Hide Winston , Szabo Gyongyi , Hecht Jonathan , Rozenblatt-Rosen Orit , Shalek Alex K. , Izar Benjamin , Regev Aviv , Popov Yury , Jiang Z. Gordon , Vlachos Ioannis S.
Published: October 2022

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.
A missense, loss-of-functionYARS1variant in a patient with proximal-predominant motor neuropathy
Authors: Forrest Megan E. , Meyer Alayne P. , Laureano Figueroa Stephanie M. , Antonellis Anthony
Published: October 2022

Aminoacyl-tRNA synthetases (ARSs) are essential enzymes with a critical role in protein synthesis: charging tRNA molecules with cognate amino acids. Heterozygosity for variants in five genes (AARS1,GARS1,HARS1,WARS1, andYARS1) encoding cytoplasmic, dimeric ARSs have been associated with autosomal dominant neurological phenotypes, including axonal Charcot–Marie–Tooth disease (CMT). Missense variants in the catalytic domain ofYARS1were previously linked to dominant intermediate CMT type C (DI-CMTC). Here, we report a patient with a missense variant of unknown significance predicted to modify residue 308 in the anticodon binding domain ofYARS1(p.Asp308Tyr). Interestingly, p.Asp308Tyr is associated with proximal-predominant motor neuropathy, which has not been reported in patients with pathogenicYARS1variants. We demonstrate that this allele causes a loss-of-function effect in yeast complementation assays when modeled inYARS1and the yeast orthologTYS1; structural modeling of this variant further supports a loss-of-function effect. Taken together, this study raises the possibility that certainYARS1variants cause proximal-prominent motor neuropathy and indicates that patients with this phenotype should be screened for genetic lesions inYARS1.
A new heteroleptic cuprous polymer constructed by a cyanopyridine ligand exhibiting a supramolecular framework structure and luminescence
Authors: Kong Yu-Jie , Wang Jian-Teng , Song Li
Published: October 2022

Luminescent cuprous complexes are of great importance among coordination compounds due to their relative abundance, low cost and ability to display excellent luminescence. The title heteroleptic cuprous polymer solvate,catena-poly[[[(9,9-dimethyl-9H-xanthene-4,5-diyl)bis(diphenylphosphane)-κ2P,P′](μ-pyridine-3-carbonitrile-κ2N1:N3)copper(I)] hexafluorophosphate dichloromethane trisolvate], {[Cu(C6H4N2)(C39H32OP2)]PF6·3CH2Cl2}n, conventionally abbreviated as {[Cu(3-PyCN)(Xantphos)]PF6·3CH2Cl2}n, where Xantphos and 3-PyCN represent (9,9-dimethyl-9H-xanthene-4,5-diyl)bis(diphenylphosphane) and pyridine-3-carbonitrile, respectively, has been described. In this polymer solvate, the asymmetric unit consists of three dichloromethane solvent molecules, a hexafluorophosphate anion and a polymeric heteroleptic cuprous complex cation, in which the cuprous centre is in a CuP2N2tetrahedral coordination and is coordinated by two P atoms from the Xantphos ligand and two N atoms from two 3-PyCN ligands (the pyridyl and cyano N atoms). It is through the connection of the μ2-bridging 3-PyCN ligand that these cuprous centres are linked into a one-dimensional helical chain structure. The chains are further assembled through C—H...π interactions to form a supramolecular metal–organic framework containing solvent-accessible channels. The UV–Vis absorption and photoluminescence properties of this heteroleptic cuprous polymer have been studied on as-synthesized samples. Its luminescence emission should mainly originate from the metal-to-ligand charge transfer excited state.
Women on boards: an empirical study on the effects on financial performance and corporate social responsibility
Authors: Awwad Bahaa Sobhi , Binsaddig Ruaa , Kanan Mohammad , Al Shirawi Thaira
Published: October 2022

Purpose

The purpose of this study is to investigate whether there is a relationship between women’s presence on boards of directors and companies’ financial performance and corporate social responsibility (CSR) disclosure and, if so, whether this relationship is positive, negative or neutral.

Design/methodology/approach

The research sample included 47 companies listed on the Palestine Stock Exchange from 2010 to 2020. Panel regression analysis was used to examine the study’s hypothesis and achieve the study’s objectives.

Findings

The presence of women on the board of directors positively affects a company’s financial performance and disclosure of CSR. However, measuring the CSR disclosure sub-components separately shows a decrease in the disclosure index towards both the environment and employees. Moreover, the level of female representation on the boards of directors of the Palestinian companies studied is generally low.

Research limitations/implications

Concerning the study limitations, the sample, which comprised all companies listed on the Palestine Stock Exchange from 2010 to 2020, was small. Concerning the implications of the study results, it is recommended that all companies listed on the Palestine Stock Exchange incorporate women on their boards of directors and in their executive management and audit committees.

Practical implications

The presence of women on Palestinian companies’ boards of directors enhances decision-making policy because of the differences between the genders as well as women’s capacity and unique skills.

Originality/value

This research contributes to the literature on women’s representation on the boards of directors of the Palestinian companies listed on the Palestine Stock Exchange with the possibility of issuing mandatory instructions for their existence. This study also attempts to provide a better understanding of the financial performance and disclosure of CSR of companies with women on these boards and helps determine whether the relationships between these variables are positive, negative or neutral. Furthermore, this study attempts to determine the extent of these companies’ commitment to the indicators of CSR disclosure.
Availability of different types of alcohol and amount of intake and next-day hangover – a naturalistic randomized controlled pilot trial
Authors: Grummedal Ole , Zangenberg Marie Strøm , Tolstrup Janne Schurmann
Published: October 2022

Purpose

The authors tested the hypothesis that having a high availability of different types of alcoholic drinks (beer, wine or spirits) as compared to being confined to one type only associate with a higher alcohol intake and worse next-day hangover.

Design/methodology/approach

This randomized controlled pilot trial took place over one evening and included 35 individuals randomized into two groups. Individuals in the mixed-type group could consume any type of alcoholic drink (beer, wine, cocktails), whereas individuals in the single-type group were to adhere to one type of own choice. Information on number of drinks was obtained continuously during the trial. Hangover symptoms were reported by participants using the Acute Hangover Severity Scale (AHSS) at 8:00, 12:00 and 16:30 the following day. Median regression was used to assess number of drinks and maximum AHSS in two groups.

Findings

Participants in the mixed-type group consumed significantly more drinks compared to the single-type group (10.9 vs 5.7, p < 0.001). The maximal AHSS score the day after drinking was higher in the mixed-type group as compared to the single-type group (median 4.3 vs 2.6, p < 0.0001).

Originality/value

This study suggests that having a variety of alcoholic drinks available associates to a higher alcohol intake and more severe hangover as compared to having to adhere to one type only. Larger studies are warranted to validate findings.
Numerical investigation of the particle circulation characteristics in a tapered fluidized bed
Authors: Che Hanqiao , Chen Tang
Published: October 2022

Purpose

The objective of this study is to investigate several issues related to particle circulation within the TFB, including exploring an appropriate method to quantify particle circulation time, the effects of different operational parameters on particle circulation time, and the relationship between particle mixing and particle circulation.

Design/methodology/approach

The computational fluid dynamics coupled with the discrete element method (CFD-DEM) is applied to investigate the particle circulation characteristics of a tapered fluidized bed (TFB). An approach for defining particle circulation, which accounts for the horizontal motion of each particle, is proposed to estimate particle circulation time.

Findings

It is found that the overall particle circulation in a TFB could be accelerated by increasing air velocity and wall inclination angle, while an increase in particle size and an increase in inter-particle cohesive forces decelerate particle circulation; the increase in the open area ratio of the central region of the air distributor would decelerate the particle circulation. Moreover, the particle circulation time and mixing rate are independent variables that describe the flow dynamics of particles from different perspectives.

Practical implications

A large part of fluidized beds in industrial applications can be classified as TFB. This study presents a numerical method to obtain detailed knowledge about particle circulation in a TFB, which is essential for the design, optimization, and control of related processes.

Originality/value

The particle circulation in a TFB is important but rarely investigated, and it is hard to be quantified using existing experimental approaches. The proposed numerical workflow reveals the characteristics of particle circulation from a particle-scale perspective.
New approach for soliton solutions for the (2 + 1)-dimensional KdV equation describing shallow water wave
Authors: Khuri Suheil
Published: October 2022

Purpose

The purpose of this study is to produce families of exact soliton solutions (2+1)-dimensional Korteweg-de Vries (KdV) equation, that describes shallow water waves, using an ansätze approach.

Design/methodology/approach

This article aims to introduce a recently developed ansätze for creating soliton and travelling wave solutions to nonlinear nonintegrable partial differential equations, especially those with physical significance.

Findings

A recently developed ansätze solution was used to successfully construct soliton solutions to the (2 + 1)-dimensional KdV equation. This straightforward method is an alternative to the Painleve test analysis, yielding similar results. The strategy demonstrated the existence of a single soliton solution, also known as a localized wave or bright soliton, as well as singular solutions or kink solitons.

Originality/value

The ansätze solution used to construct soliton solutions to the (2 + 1)-dimensional KdV equation is novel. New soliton solutions were also obtained.
Advancing the institutional perspective on informal entrepreneurship: a study of formalization intentions among street entrepreneurs
Authors: Shahid Muhammad Shehryar , Rodgers Peter , Vershinina Natalia , Zehra Mashal E. , Williams Colin C.
Published: October 2022

Purpose

Informal entrepreneurship is seen as a direct outcome of either the failure of formal institutions or the asymmetry between formal and informal institutions. These two viewpoints are so far debated as alternative theoretical explanations for the prevalence of informal entrepreneurship. In this paper, the authors offer a theoretically integrative approach to further advance the institutional perspective of informal entrepreneurship. The purpose of this paper is to address these issues.

Design/methodology/approach

Using face-to-face surveys of 322 street entrepreneurs from Lahore, Pakistan, the authors deploy the hitherto unused partial least square approach (PLS) to structural equation modeling (SEM) to analyze data within the field of informal entrepreneurship.

Findings

The empirical findings strongly support the theoretical propositions of the new institutional perspective that the authors present in their paper. The authors find no direct impact of factors like procedural justice, redistributive justice and public sector corruption (i.e. formal institutional failings) on the formalization intentions of street entrepreneurs. Their findings demonstrate that the relationship between formal institutional failings and formalization intentions can only be explained through the mediating role of institutional asymmetry (i.e. tax morality).

Research limitations/implications

From a policy perspective, the authors find that if they can encourage street entrepreneurs to obtain a local-level registration as the first step toward formalization, it will significantly increase their chances to opt for higher national-level registrations.

Originality/value

This paper presents a unique attempt to further understand the context of street entrepreneurship through the theoretical lens of the institutional theory. In doing so, it synthesizes the arguments of existing institutional perspectives and further develops the institutional theory of informal entrepreneurship. Moreover, the paper develops the concept of “formalization intentions”.
Beyond the certification of smart tourism destination: insights from the city of Medellín in Colombia
Authors: Aïdi Naïma , Fabry Nathalie
Published: October 2022

Purpose

This paper aims to give meaning to the smart tourism destination (STD) certification, highlighting its main advantages and limitations. The case of Medellín (Colombia) presents characteristics worth studying. The city has suffered from stigmatization and has recently started the steps to become an STD with the Spanish company Segittur (December 2020). Thus, this study aims to focus on the implications of the STD process, especially in an area that has been impacted by tourist activity.

Design/methodology/approach

This paper is a qualitative and exploratory case study about Medellín in Colombia and its tourism development in an STD framework. After a theoretical exploration of the STD from an urban perspective, the paper will present a multiple data corpus to analyze the city’s certification process to turn into an STD. This methodology explores stakeholders on the destination, including an observation, and allows us to obtain an overview of the implications of the STD certification for Medellín.

Findings

During the past decade, Medellín passed from a dangerous destination to a trendy destination. Findings reveal interesting results, considering the need to consider all aspects of territory as a central issue for the STD settlement and look beyond a technological approach.

Originality/value

This paper lets to understand better the STD process established by the institution. Moreover, it highlights the gap between the coveted certification to become the first STD in Colombia and the realities of a Latin American territory.
“Playing tourist” in a divided city
Authors: Lindblom Jada , Vogt Christine
Published: October 2022

Purpose

This study aims to investigate the social and affective impacts of inviting residents of a socially divided, post-war city to “play tourist” for a day, exploring their own backyards with a new intentionality and perspective.

Design/methodology/approach

This qualitative research within a transformative worldview uses a creative, place-based approach of role-playing based upon principles of participatory action research.

Findings

While each tour was unique, participants’ insights reflected three common themes: shifts in observations and perceptions of place arising from the intentionality of the “tourist” lens, a sense of freedom created by the touristic research opportunity, and the varying abilities of tourism experiences to help build empathy or awareness in a post-conflict setting.

Originality/value

The inventive research approach allows for a unique examination of local tourism-styled explorations, a subject of growing interest that has largely been overlooked in literature, while paying special attention to ways in which a history of conflict may manifest in contemporary urban tourism experiences.