bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alteration of a brain network with stable and strong functional connections in subjects with schizophrenia
Authors: Yuan Liu , Ma Xiaoqian , Li David , Ouyang Lijun , Fan Lejia , Li Chunwang , He Ying , Chen Xiaogang 
Published: November 2022

AbstractIt is widely accepted that there are some common network patterns in the human brain. However, the existence of stable and strong functional connections in the human brain and whether they change in schizophrenia is still a question. By setting 1% connections with the smallest coefficient of variation, we found a widespread brain functional network (frame network) in healthy people(n = 380, two datasets from public databases). We then explored the alterations in a medicated group (60 subjects with schizophrenia vs 71 matched controls) and a drug-naive first-episode group (68 subjects with schizophrenia vs 45 matched controls). A linear support vector classifier (SVC) was constructed to distinguish patients and controls using the medicated patients’ frame network. We found most frame connections of healthy people had high strength, which were symmetrical and connected the left and right hemispheres. Conversely, significant differences in frame connections were observed in both patient groups, which were positively correlated with negative symptoms (mainly language dysfunction). Additionally, patients’ frame network were more left-lateralized, concentrating on the left frontal lobe, and was quite accurate at distinguishing medicated patients from controls (classifier accuracy was 78.63%, sensitivity was 86.67%, specificity was 76.06%, and the area under the curve (AUC) was 0.83). Furthermore, the results were repeated in the drug-naive set (accuracy was 84.96%, sensitivity was 85.29%, specificity was 88.89%, and AUC was 0.93). These findings indicate that the abnormal pattern of frame network in subjects with schizophrenia might provide new insights into the dysconnectivity in schizophrenia.
Creation and preclinical evaluation of genetically attenuated malaria parasites arresting growth late in the liver
Authors: Franke-Fayard Blandine , Marin-Mogollon Catherin , Geurten Fiona J. A. , Chevalley-Maurel Séverine , Ramesar Jai , Kroeze Hans , Baalbergen Els , Wessels Els , Baron Ludivine , Soulard Valérie , Martinson Thomas , Aleshnick Maya , Huijs Antonius T. G. , Subudhi Amit K. , Miyazaki Yukiko , Othman Ahmad Syibli , Kolli Surendra Kumar , Lamers Olivia A. C. , Roques Magali , Stanway Rebecca R. , Murphy Sean C. , Foquet Lander , Moita Diana , Mendes António M. , Prudêncio Miguel , Dechering Koen J. , Heussler Volker T. , Pain Arnab , Wilder Brandon K. , Roestenberg Meta , Janse Chris J. 
Published: November 2022

AbstractWhole-sporozoite (WSp) malaria vaccines induce protective immune responses in animal malaria models and in humans. A recent clinical trial with a WSp vaccine comprising genetically attenuated parasites (GAP) which arrest growth early in the liver (PfSPZ-GA1), showed that GAPs can be safely administered to humans and immunogenicity is comparable to radiation-attenuated PfSPZ Vaccine. GAPs that arrest late in the liver stage (LA-GAP) have potential for increased potency as shown in rodent malaria models. Here we describe the generation of four putative P. falciparum LA-GAPs, generated by CRISPR/Cas9-mediated gene deletion. One out of four gene-deletion mutants produced sporozoites in sufficient numbers for further preclinical evaluation. This mutant, PfΔmei2, lacking the mei2-like RNA gene, showed late liver growth arrest in human liver-chimeric mice with human erythrocytes, absence of unwanted genetic alterations and sensitivity to antimalarial drugs. These features of PfΔmei2 make it a promising vaccine candidate, supporting further clinical evaluation. PfΔmei2 (GA2) has passed regulatory approval for safety and efficacy testing in humans based on the findings reported in this study.
Metabolomics profiling in acute liver transplant rejection in a pediatric population
Authors: Frediani Jennifer K. , Beyh Yara S. , Gupta Nitika , Westbrook Adrianna L. , Cleeton Rebecca , Cordero Maria , Hernandez Albert , Tran ViLinh , Jones Dean P. , Vos Miriam B. 
Published: November 2022

AbstractPediatric liver transplantation rejection affects 20% of children. Currently, liver biopsy, expensive and invasive, is the best method of diagnosis. Discovery and validation of clinical biomarkers from blood or other biospecimens would improve clinical care. For this study, stored plasma samples were utilized from two cross-sectional cohorts of liver transplant patients at Children’s Healthcare of Atlanta. High resolution metabolic profiling was completed using established methods. Children with (n = 18) or without (n = 25) acute cellular rejection were included in the analysis (n = 43 total). The mean age of these racially diverse cohorts ranged from 12.6 years in the rejection group and 13.6 years in the no rejection group. Linear regression provided 510 significantly differentiating metabolites between groups, and OPLS-DA showed 145 metabolites with VIP > 2. A total of 95 overlapping significant metabolites between OPLS-DA and linear regression analyses were detected. Pathway analysis (p < 0.05) showed bile acid biosynthesis and tryptophan metabolism as the top two differentiating pathways. Network analysis also identified tryptophan and clustered with liver enzymes and steroid use. We conclude metabolic profiling of plasma from children with acute liver transplant rejection demonstrates > 500 significant metabolites. This result suggests that development of a non-invasive biomarker-based test is possible for rejection screening.
Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework
Authors: Heuts B. M. H. , Arza-Apalategi S. , Frölich S. , Bergevoet S. M. , van den Oever S. N. , van Heeringen S. J. , van der Reijden B. A. , Martens J. H. A. 
Published: November 2022

AbstractAdvanced computational methods exploit gene expression and epigenetic datasets to predict gene regulatory networks controlled by transcription factors (TFs). These methods have identified cell fate determining TFs but require large amounts of reference data and experimental expertise. Here, we present an easy to use network-based computational framework that exploits enhancers defined by bidirectional transcription, using as sole input CAGE sequencing data to correctly predict TFs key to various human cell types. Next, we applied this Analysis Algorithm for Networks Specified by Enhancers based on CAGE (ANANSE-CAGE) to predict TFs driving red and white blood cell development, and THP-1 leukemia cell immortalization. Further, we predicted TFs that are differentially important to either cell line- or primary- associated MLL-AF9-driven gene programs, and in primary MLL-AF9 acute leukemia. Our approach identified experimentally validated as well as thus far unexplored TFs in these processes. ANANSE-CAGE will be useful to identify transcription factors that are key to any cell fate change using only CAGE-seq data as input.
A randomized multicenter evaluation of the efficacy of 0.15% hyaluronic acid versus 0.05% cyclosporine A in dry eye syndrome
Authors: Lee Ji Eun , Kim Sangyoon , Lee Hyung Keun , Chung Tae-Young , Kim Jae Yong , Choi Chul Young , Chung So Hyang , Kim Dong Hyun , Kim Kyoung Woo , Chung Jin Kwon , Hwang Kyu Yeon , Hwang Ho Sik , Kim Jin Hyoung , Hyon Joon Young 
Published: November 2022

AbstractHyaluronic acid (HA) and cyclosporine A (CsA) eyedrops are commonly prescribed in dry eye syndrome (DES). The effectiveness of each preparation in DES is well-known, yet the superiority of one over another has been studied little. We assessed the efficacy and tolerability of 0.15% HA compared to combinations of 0.05% CsA plus 0.5% carboxymethylcellulose (CMC), and 0.15% HA plus 0.05% CsA in patients with moderate to severe DES. Total 438 patients with moderate to severe DES were recruited and randomized for one of the three treatments for 12 weeks. Effectiveness was assessed at baseline, 4- and 12-weeks. The primary endpoint was change in corneal staining score. The secondary endpoints were tear break-up time (TBUT), strip meniscometry (SM) score, ocular surface disease index (OSDI) score, and tolerability questionnaire. The change in corneal staining score for 0.15% HA from the baseline was non-inferior to that of 0.05% CsA. Corneal staining score, TBUT, SM score, and OSDI score improved in all groups without statistically significant intergroup differences. Better tolerability and lower prevalence of adverse drug reactions were seen in 0.15% HA. Our findings suggest that 0.15% HA may be equivalently effective and safer than 0.05% CsA in treating moderate to severe DES.
The dominant mesopredator and savanna formations shape the distribution of the rare northern tiger cat (Leopardus tigrinus) in the Amazon
Authors: de Oliveira Tadeu G. , Fox-Rosales Lester A. , Paemelaere Evi A. D. , de Barros Ferraz Katia Maria Paschoaletto Micchi 
Published: November 2022

AbstractUnderstanding the distribution patterns of threatened species is central to conservation. The Amazonian distribution of the northern tiger cat (N-tiger cat, Leopardus tigrinus) and its interspecific relationship with the ocelot, its potential intraguild killer, are intriguing. Here, we combined presence/absence records with species distribution models (SDMs) to determine N-tiger cat occurrence in the Amazon. We also modeled ocelot density from 46 published estimates. The N-tiger cat’s presence in the Amazon was negatively influenced by ocelot density and net primary productivity and positively influenced by savannas and precipitation in the driest month. The best-fitting model predicted highly patchy N-tiger cat occurrence over an area of 236,238.67 km2, almost exclusively in savanna enclaves. Additionally, 312,348 camera trap-days at 49 sites in the Amazon revealed no N-tiger cats. The ocelot densities were significantly higher in areas with denser vegetation cover and warmer habitats, with predicted densities ≥ 0.6 ind/km2 throughout most of the biome. The lowest ocelot densities (≤ 0.06 ind/km2) were observed along the predicted range of N-tiger cats. Our findings highlight that the N-tiger cat’s presence in the Amazon is restricted to savannas and highly influenced by ocelot density, emphasizing the importance of including species interactions in SDMs.
Crystal structure thermal evolution and novel orthorhombic phase of methylammonium lead bromide, CH3NH3PbBr3
Authors: Abia Carmen , López Carlos A. , Cañadillas-Delgado Laura , Fernández-Diaz María T. , Alonso José A. 
Published: November 2022

AbstractMethylammonium (MA) lead trihalide perovskites, CH3NH3PbX3 (X = I, Br, Cl), have emerged as a new class of light-absorbing materials for photovoltaic applications, reaching efficiencies of 23% when implemented in solar cell heterojunctions. In particular, MAPbBr3 is a promising member with a large bandgap that gives rise to a high open circuit voltage. Here we present a structural study from neutron diffraction (ND) data of an undeuterated MAPbBr3 specimen, carried out to follow its crystallographic behaviour in the 2–298 K temperature range. Besides the known crystallographic phases, i.e. the high-temperature Pm$$\overline{3}$$

3
¯

m cubic structure, the intermediate I4/mcm tetragonal symmetry and the low-temperature Pnma orthorhombic phase, we additionally identified, from a detailed sequential ND analysis, a novel intermediate phase within the 148.5–154.0 K temperature range as an orthorhombic Imma structure, early associated with a coexistence of phases. Moreover, our ND data allowed us to unveil the configuration of the organic MA units and their complete localization within the mentioned temperature range, thus improving the crystallographic description of this compound. The evolution with temperature of the H-bonds between the organic molecule and the inorganic cage is also followed. A deep knowledge of the crystal structure and, in particular, the MA conformation inside the perovskite cage seems essential to establish structure–property correlations that may drive further improvements.
Engineered living photosynthetic biocomposites for intensified biological carbon capture
Authors: In-na Pichaya , Sharp Elliot B. , Caldwell Gary S. , Unthank Matthew G. , Perry Justin J. , Lee Jonathan G. M. 
Published: November 2022

AbstractCarbon capture and storage is required to meet Paris Agreement targets. Photosynthesis is nature’s carbon capture technology. Drawing inspiration from lichen, we engineered 3D photosynthetic cyanobacterial biocomposites (i.e., lichen mimics) using acrylic latex polymers applied to loofah sponge. Biocomposites had CO2 uptake rates of 1.57 ± 0.08 g CO2 g−1biomass d−1. Uptake rates were based on the dry biomass at the start of the trial and incorporate the CO2 used to grow new biomass as well as that contained in storage compounds such as carbohydrates. These uptake rates represent 14–20-fold improvements over suspension controls, potentially scaling to capture 570 tCO2 t−1biomass yr−1, with an equivalent land consumption of 5.5–8.17 × 106 ha, delivering annualized CO2 removal of 8–12 GtCO2, compared with 0.4–1.2 × 109 ha for forestry-based bioenergy with carbon capture and storage. The biocomposites remained functional for 12 weeks without additional nutrient or water supplementation, whereupon experiments were terminated. Engineered and optimized cyanobacteria biocomposites have potential for sustainable scalable deployment as part of humanity’s multifaceted technological stand against climate change, offering enhanced CO2 removal with low water, nutrient, and land use penalties.
Monopole directional antenna bioinspired in elliptical leaf with golden ratio for WLAN and 4G applications
Authors: Froes Eduarda , Silva Junior Paulo F. , Santana Ewaldo E. C. , Sousa Junior Carlos M. , Silva Paulo H. F. , Cruz Carlos A. M. , Aquino Vivianne S. , Castro Luis S. O. , Freire Raimundo C. S. , Pinto Mauro S. S. 
Published: November 2022

AbstractIn this work, it is proposed the development a new monopole directional antenna, bioinspired in elliptical leaf, with cut by golden ratio, for 4G band application, by the use of the technique of the cut of the radiating element for the increasing of the antenna perimeter, being the first work to use this technique in a bioinspired antenna, promotes resonance frequency turned, and reconfiguring of the antenna parameters as bandwidth, radiation pattern and gain, with the use of the reflector near to the group plane, without the insertion of active devices as the pin diode or change in radiating element. The shape antenna is generated by Gielis formula, built in FR4 substrate, with cuts calculated by golden ratio. To compare the results of the bioinspired monopole on the elliptical sheet, a square-shaped monopole antenna was designed, simulated and measured, the structures were designed in the MATLAB software version 2015(b) and the simulations were performed in the Ansys software version 2016. In the results compared between the square monopole and the bioinspired antenna in the elliptical sheet, it can be seen that the measured bioinspired antenna, compared to the square monopole, presented a bandwidth reduction of 77.27%, a more compact structure, with a reduction of 98%, covering the wireless local area network, and long-time evolution 4G at 2.5 GHz. The proposed technique uses a reflector on the ground plane, to change the parameters of the monopole planar antenna, of omnidirectional radiation pattern to a directional, maintaining the characteristics of the broadband, half-power beamwidth great than 100°, with high current density, and similar gain of a directional antenna. From the results, it has been observed that the elliptical leaf monopole antenna shows broadband characteristics, with a half-power beamwidth of 128°, wideband, the bandwidth of 500 MHz, a gain of 6.28 dBi, a current density of 13.01 A/m2, and circular polarization.
Site-specific CRISPR-based mitochondrial DNA manipulation is limited by gRNA import
Authors: Schmiderer Ludwig , Yudovich David , Oburoglu Leal , Hjort Martin , Larsson Jonas 
Published: November 2022

AbstractAchieving CRISPR Cas9-based manipulation of mitochondrial DNA (mtDNA) has been a long-standing goal and would be of great relevance for disease modeling and for clinical applications. In this project, we aimed to deliver Cas9 into the mitochondria of human cells and analyzed Cas9-induced mtDNA cleavage and measured the resulting mtDNA depletion with multiplexed qPCR. In initial experiments, we found that measuring subtle effects on mtDNA copy numbers is challenging because of high biological variability, and detected no significant Cas9-caused mtDNA degradation. To overcome the challenge of being able to detect Cas9 activity on mtDNA, we delivered cytosine base editor Cas9-BE3 to mitochondria and measured its effect (C →  T mutations) on mtDNA. Unlike regular Cas9-cutting, this leaves a permanent mark on mtDNA that can be detected with amplicon sequencing, even if the efficiency is low. We detected low levels of C → T mutations in cells that were exposed to mitochondrially targeted Cas9-BE3, but, surprisingly, these occurred regardless of whether a guide RNA (gRNA) specific to the targeted site, or non-targeting gRNA was used. This unspecific off-target activity shows that Cas9-BE3 can technically edit mtDNA, but also strongly indicates that gRNA import to mitochondria was not successful. Going forward mitochondria-targeted Cas9 base editors will be a useful tool for validating successful gRNA delivery to mitochondria without the ambiguity of approaches that rely on quantifying mtDNA copy numbers.
Identification of mutations in SARS-CoV-2 PCR primer regions
Authors: Mentes Anikó , Papp Krisztián , Visontai Dávid , Stéger József ,   VEO Technical Working Group, Csabai István , Papp Krisztián , Visontai Dávid , Stéger József , Cochrane Guy , Rahman Nadim , Cummins Carla , Yuan David Yu , Selvakumar Sandeep , Mansurova Milena , O’Cathail Colman , Sokolov Alexey , Thorne Ross , Koopmans Marion , Nieuwenhuijse David , Oude-Munnink Bas , Worp Nathalie , Amid Clara , Csabai István , Medgyes-Horváth Anna , Pipek Orsolya Anna 
Published: November 2022

AbstractDue to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as “prone to misclassification” vs. “likely to be correctly detected” by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.
Trophic provisioning and parental trade-offs lead to successful reproductive performance in corals after a bleaching event
Authors: Rodrigues Lisa J. , Padilla-Gamiño Jacqueline L. 
Published: November 2022

AbstractWarming ocean temperatures are severely compromising the health and resilience of coral reefs worldwide. Coral bleaching can affect coral physiology and the energy available for corals to reproduce. Mechanisms associated with reproductive allocation in corals are poorly understood, especially after a bleaching event occurs. Using isotopic labeling techniques, we traced the acquisition and allocation of carbon from adults to gametes by autotrophy and heterotrophy in previously bleached and non-bleachedMontipora capitataandPorites compressacorals. Experiments revealed that both species: (1) relied only on autotrophy to allocate carbon to gametes, while heterotrophy was less relied upon as a carbon source; (2) experienced a trade-off with less carbon available for adult tissues when provisioning gametes, especially when previously bleached; and (3) used different strategies for allocating carbon to gametes. Over time,M. capitataallocated 10% more carbon to gametes despite bleaching by limiting the allocation of carbon to adult tissues, with 50–80% less carbon allocated to bleached compared to non-bleached colonies. Over the same time period,P. compressamaintained carbon allocation to adult tissues, before allocating carbon to gametes. Our study highlights the importance of autotrophy for carbon allocation from adult corals to gametes, and species-specific differences in carbon allocation depending on bleaching susceptibility.
Anemia, iron deficiency, and thalassemia among the Thai population inhabiting at the Thailand-Lao PDR-Cambodia triangle
Authors: Karnpean Rossarin , Vanichakulthada Nawinda , Suwannaloet Wanwisa , Thongrung Ruttiya , Singsanan Sanita , Prakobkaew Nattapol , Fucharoen Goonnapa , Fucharoen Supan 
Published: November 2022

AbstractAnemia is a major public health problem in many areas of Southeast Asia. Ascertaining anemia and defining its underlying causes is essential for providing appropriate care, management, and establishment of a control program. Limited studies on these have been carried out on people living at the borders of Thailand, Lao PDR, and Cambodia. This cross-sectional study was done in four areas along the borders of Thailand, Lao PDR, and Cambodia. Blood specimens were collected from subjects aged 15–18 years in four districts including Kantharalak, Si Sa Ket province (n = 36), Nam Khun (n = 109), Nam Yuen (n = 98), and Na Chaluai (n = 128), Ubon Ratchathani province, Thailand. RBC parameters were recorded, and serum ferritin (SF) level was measured. Diagnosis of thalassemia and hemoglobinopathies was based on hemoglobin (Hb) and DNA analyses. Measurement of C-reactive protein was performed to exclude false-negative result of iron deficiency. The prevalence of anemia was found to be 25.1%. ID accounted for only 10.5%. Various types of thalassemia were identified in 67.7% of the subjects. The overall prevalence of thalassemia included 3.5% α0-thalassemia, 0.8% β-thalassemia, 47.7% Hb E, and 53.6% α+-thalassemia. The proportions of ID, thalassemia and combined ID and thalassemia among anemic subjects were 6.5%, 66.6%, and 20.4%, respectively. The results indicate that thalassemia and hemoglobinopathies rather than ID are major causes of anemia in Thailand-Lao PDR-Cambodia triangle. This information should prove useful for implementing an anemia control program in the regions.