bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of tryptophan depletion on anxiety, a systematic review
Authors: Schopman Simone M. E. , Bosman Renske C. , Muntingh Anna D. T. , van Balkom Anton J. L. M. , Batelaan Neeltje M. 
Published: February 2021

AbstractVulnerability markers for onset of anxiety disorders are scarce. In depression, patients at risk tend to respond with a negative mood to ‘acute tryptophan depletion’ (ATD), while healthy volunteers and current patients do not. The serotonergic system thus provides indications for vulnerability for depression. It is unknown whether ATD reveals vulnerability in anxiety too. This study systematically reviews the effects of ATD on anxiety and assesses whether challenging anxiety modifies the response. PubMed, Embase and PsychInfo were systematically searched up to April 2019 for studies in which (1) healthy volunteers or patients with a (remitted) anxiety disorder underwent ATD and (2) levels of anxiety were reported. In total, 21 studies were included. Studies conducted in healthy volunteers (n = 13), and patients with a remitted (n = 6) or current (panic, social or generalised) anxiety disorder (n = 4). Studies were mostly of poor quality and heterogeneous regarding population, challenge test used and outcome measures. ATD did not consistently affect anxiety in any of the groups. Moreover, a challenge test after ATD (n = 17 studies) did not consistently provoke anxiety in healthy volunteers or remitted patients. A 35% CO2 challenge did consistently increase anxiety in patients with a current panic disorder (PD). To conclude, this systematic review found no clear indications that ATD provokes anxiety in those at risk for anxiety disorders. Hence, unlike in depression, ATD does not indicate vulnerability to develop an anxiety disorder. Because included studies were heterogeneous and mostly of poor quality, there is an urgent need for high quality research in homogeneous samples.
Silane- and peroxide-free hydrogen atom transfer hydrogenation using ascorbic acid and cobalt-photoredox dual catalysis
Authors: Kamei Yuji , Seino Yusuke , Yamaguchi Yuto , Yoshino Tatsuhiko , Maeda Satoshi , Kojima Masahiro , Matsunaga Shigeki 
Published: February 2021

AbstractHydrogen atom transfer (HAT) hydrogenation has recently emerged as an indispensable method for the chemoselective reduction of unactivated alkenes. However, the hitherto reported systems basically require stoichiometric amounts of silanes and peroxides, which prevents wider applications, especially with respect to sustainability and safety concerns. Herein, we report a silane- and peroxide-free HAT hydrogenation using a combined cobalt/photoredox catalysis and ascorbic acid (vitamin C) as a sole stoichiometric reactant. A cobalt salophen complex is identified as the optimal cocatalyst for this environmentally benign HAT hydrogenation in aqueous media, which exhibits high functional-group tolerance. In addition to its applicability in the late-stage hydrogenation of amino-acid derivatives and drug molecules, this method offers unique advantage in direct transformation of unprotected sugar derivatives and allows the HAT hydrogenation of unprotected C-glycoside in higher yield compared to previously reported HAT hydrogenation protocols. The proposed mechanism is supported by experimental and theoretical studies.
Terahertz-field-induced polar charge order in electronic-type dielectrics
Authors: Yamakawa H. , Miyamoto T. , Morimoto T. , Takamura N. , Liang S. , Yoshimochi H. , Terashige T. , Kida N. , Suda M. , Yamamoto H. M. , Mori H. , Miyagawa K. , Kanoda K. , Okamoto H. 
Published: February 2021

AbstractUltrafast electronic-phase change in solids by light, called photoinduced phase transition, is a central issue in the field of non-equilibrium quantum physics, which has been developed very recently. In most of those phenomena, charge or spin orders in an original phase are melted by photocarrier generations, while an ordered state is usually difficult to be created from a non-ordered state by a photoexcitation. Here, we demonstrate that a strong terahertz electric-field pulse changes a Mott insulator of an organic molecular compound in κ-(ET)2Cu[N(CN)2]Cl (ET = bis(ethylenedithio)tetrathiafulvalene), to a macroscopically polarized charge-order state; herein, electronic ferroelectricity is induced by the collective intermolecular charge transfers in each dimer. In contrast, in an isostructural compound, κ-(ET)2Cu2(CN)3, which shows the spin-liquid state at low temperatures, a similar polar charge order is not stabilized by the same terahertz pulse. From the comparative studies of terahertz-field-induced second-harmonic-generation and reflectivity changes in the two compounds, we suggest the possibility that a coupling of charge and spin degrees of freedom would play important roles in the stabilization of polar charge order.
Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions
Authors: Bi Yang , Deng Zhiping , Ni Weimin , Shrestha Ruben , Savage Dasha , Hartwig Thomas , Patil Sunita , Hong Su Hyun , Zhang Zhenzhen , Oses-Prieto Juan A. , Li Kathy H. , Quail Peter H. , Burlingame Alma L. , Xu Shou-Ling , Wang Zhi-Yong 
Published: February 2021

AbstractO-GlcNAc modification plays important roles in metabolic regulation of cellular status. Two homologs of O-GlcNAc transferase, SECRET AGENT (SEC) and SPINDLY (SPY), which have O-GlcNAc and O-fucosyl transferase activities, respectively, are essential in Arabidopsis but have largely unknown cellular targets. Here we show that AtACINUS is O-GlcNAcylated and O-fucosylated and mediates regulation of transcription, alternative splicing (AS), and developmental transitions. Knocking-out both AtACINUS and its distant paralog AtPININ causes severe growth defects including dwarfism, delayed seed germination and flowering, and abscisic acid (ABA) hypersensitivity. Transcriptomic and protein-DNA/RNA interaction analyses demonstrate that AtACINUS represses transcription of the flowering repressor FLC and mediates AS of ABH1 and HAB1, two negative regulators of ABA signaling. Proteomic analyses show AtACINUS’s O-GlcNAcylation, O-fucosylation, and association with splicing factors, chromatin remodelers, and transcriptional regulators. Some AtACINUS/AtPININ-dependent AS events are altered in the sec and spy mutants, demonstrating a function of O-glycosylation in regulating alternative RNA splicing.
Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase
Authors: Bellin Leo , Del Caño-Ochoa Francisco , Velázquez-Campoy Adrián , Möhlmann Torsten , Ramón-Maiques Santiago 
Published: February 2021

AbstractAspartate transcarbamoylase (ATC), an essential enzyme for de novo pyrimidine biosynthesis, is uniquely regulated in plants by feedback inhibition of uridine 5-monophosphate (UMP). Despite its importance in plant growth, the structure of this UMP-controlled ATC and the regulatory mechanism remain unknown. Here, we report the crystal structures of Arabidopsis ATC trimer free and bound to UMP, complexed to a transition-state analog or bearing a mutation that turns the enzyme insensitive to UMP. We found that UMP binds and blocks the ATC active site, directly competing with the binding of the substrates. We also prove that UMP recognition relies on a loop exclusively conserved in plants that is also responsible for the sequential firing of the active sites. In this work, we describe unique regulatory and catalytic properties of plant ATCs that could be exploited to modulate de novo pyrimidine synthesis and plant growth.
Methodological quality of COVID-19 clinical research
Authors: Jung Richard G. , Di Santo Pietro , Clifford Cole , Prosperi-Porta Graeme , Skanes Stephanie , Hung Annie , Parlow Simon , Visintini Sarah , Ramirez F. Daniel , Simard Trevor , Hibbert Benjamin 
Published: February 2021

AbstractThe COVID-19 pandemic began in early 2020 with major health consequences. While a need to disseminate information to the medical community and general public was paramount, concerns have been raised regarding the scientific rigor in published reports. We performed a systematic review to evaluate the methodological quality of currently available COVID-19 studies compared to historical controls. A total of 9895 titles and abstracts were screened and 686 COVID-19 articles were included in the final analysis. Comparative analysis of COVID-19 to historical articles reveals a shorter time to acceptance (13.0[IQR, 5.0–25.0] days vs. 110.0[IQR, 71.0–156.0] days in COVID-19 and control articles, respectively; p < 0.0001). Furthermore, methodological quality scores are lower in COVID-19 articles across all study designs. COVID-19 clinical studies have a shorter time to publication and have lower methodological quality scores than control studies in the same journal. These studies should be revisited with the emergence of stronger evidence.
COPD awareness in the urban slums and rural areas around Pune city in India
Authors: Ghorpade Deesha Deepak , Raghupathy Anchala , Londhe Jyoti Deepak , Madas Sapna Jitendra , Kale Nisha Vijay , Singh Narula Arvinder Pal , Patil Reshma Sudhir , Barne Monica Sumit , Doke Prakash Prabhakar Rao , Salvi Sundeep Santosh 
Published: February 2021

AbstractCOPD is the second leading cause of death and disability adjusted life years (DALYs) in India, yet, it remains poorly recognized. We aimed to study the level of awareness of COPD in urban slums of Pune city in India and its neighboring rural areas. All male and female subjects above the age of 30 years residing in 13 randomly selected slums of Pune city (total population of 3000) and 7 randomly selected neighboring rural villages (total population of 3000) were invited to participate in this cross-sectional community survey. After obtaining written informed consent, 13 trained community health workers (CHWs) administered a questionnaire that captured their level of awareness of COPD. Of the 6000 subjects approached, 5420 residents (mean age ± SD = 48.0 ± 13.5 years; 38% males) consented and answered all questions. The number of people who had ever heard the word COPD was 49/5420 [0.9% (0.6–1.1%); 0.7% (0.5–1.3%) of the urban slum dwellers and 1.15% (0.5–1.3%) of rural residents]. Among those who had never heard the word COPD (n = 5371), when asked what was the name of the disease caused by long-term tobacco smoking, 38% said cancer, 16.7% said asthma, and 4.4% said TB. Among those who had heard the word COPD (n = 49), 6.1% said it was a disease of the heart, and 61% attributed COPD to smoke and dust pollution and 20% to tobacco smoking. The level of awareness of COPD in the Indian community is extremely low, highlighting the need to have nationwide mass awareness programs in India.
Promoting versatile vaccine development for emerging pandemics
Authors: Monrad Joshua T. , Sandbrink Jonas B. , Cherian Neil G. 
Published: February 2021

AbstractThe ongoing COVID-19 pandemic has demonstrated the importance of rapid and versatile development of emergency medical countermeasures such as vaccines. We discuss the role of platform vaccines and prototype pathogen research in modern vaccine development, and outline how previous pathogen-specific funding approaches can be improved to adequately promote vaccine R&D for emerging pandemics. We present a more comprehensive approach to financing vaccine R&D, which maximises biomedical pandemic preparedness by promoting flexible vaccine platforms and translatable research into prototype pathogens. As the numerous platform-based SARS-CoV-2 vaccines show, funders can accelerate pandemic vaccine development by proactively investing in versatile platform technologies. For certain emerging infectious diseases, where vaccine research can translate to other related pathogens with pandemic potential, investment decisions should reflect the full social value of increasing overall preparedness, rather than just the value of bringing a vaccine to market for individual pathogens.
Collegiate athlete brain data for white matter mapping and network neuroscience
Authors: Caron Bradley , Stuck Ricardo , McPherson Brent , Bullock Daniel , Kitchell Lindsey , Faskowitz Joshua , Kellar Derek , Cheng Hu , Newman Sharlene , Port Nicholas , Pestilli Franco 
Published: February 2021

AbstractWe describe a dataset of processed data with associated reproducible preprocessing pipeline collected from two collegiate athlete groups and one non-athlete group. The dataset shares minimally processed diffusion-weighted magnetic resonance imaging (dMRI) data, three models of the diffusion signal in the voxel, full-brain tractograms, segmentation of the major white matter tracts as well as structural connectivity matrices. There is currently a paucity of similar datasets openly shared. Furthermore, major challenges are associated with collecting this type of data. The data and derivatives shared here can be used as a reference to study the effects of long-term exposure to collegiate athletics, such as the effects of repetitive head impacts. We use advanced anatomical and dMRI data processing methods publicly available as reproducible web services at brainlife.io.
Computational scanning tunneling microscope image database
Authors: Choudhary Kamal , Garrity Kevin F. , Camp Charles , Kalinin Sergei V. , Vasudevan Rama , Ziatdinov Maxim , Tavazza Francesca 
Published: February 2021

AbstractWe introduce the systematic database of scanning tunneling microscope (STM) images obtained using density functional theory (DFT) for two-dimensional (2D) materials, calculated using the Tersoff-Hamann method. It currently contains data for 716 exfoliable 2D materials. Examples of the five possible Bravais lattice types for 2D materials and their Fourier-transforms are discussed. All the computational STM images generated in this work are made available on the JARVIS-STM website (https://jarvis.nist.gov/jarvisstm). We find excellent qualitative agreement between the computational and experimental STM images for selected materials. As a first example application of this database, we train a convolution neural network model to identify the Bravais lattice from the STM images. We believe the model can aid high-throughput experimental data analysis. These computational STM images can directly aid the identification of phases, analyzing defects and lattice-distortions in experimental STM images, as well as be incorporated in the autonomous experiment workflows.
Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations
Authors: Syuhada Ibnu , Hauwali Nikodemus Umbu Janga , Rosikhin Ahmad , Sustini Euis , Noor Fatimah Arofiati , Winata Toto 
Published: February 2021

AbstractIn this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.
Long-QT founder variant T309I-Kv7.1 with dominant negative pattern may predispose delayed afterdepolarizations under β-adrenergic stimulation
Authors: Synková Iva , Bébarová Markéta , Andršová Irena , Chmelikova Larisa , Švecová Olga , Hošek Jan , Pásek Michal , Vít Pavel , Valášková Iveta , Gaillyová Renata , Navrátil Rostislav , Novotný Tomáš 
Published: February 2021

AbstractThe variant c.926C > T (p.T309I) in KCNQ1 gene was identified in 10 putatively unrelated Czech families with long QT syndrome (LQTS). Mutation carriers (24 heterozygous individuals) were more symptomatic compared to their non-affected relatives (17 individuals). The carriers showed a mild LQTS phenotype including a longer QTc interval at rest (466 ± 24 ms vs. 418 ± 20 ms) and after exercise (508 ± 32 ms vs. 417 ± 24 ms), 4 syncopes and 2 aborted cardiac arrests. The same haplotype associated with the c.926C > T variant was identified in all probands. Using the whole cell patch clamp technique and confocal microscopy, a complete loss of channel function was revealed in the homozygous setting, caused by an impaired channel trafficking. Dominant negativity with preserved reactivity to β-adrenergic stimulation was apparent in the heterozygous setting. In simulations on a human ventricular cell model, the dysfunction resulted in delayed afterdepolarizations (DADs) and premature action potentials under β-adrenergic stimulation that could be prevented by a slight inhibition of calcium current. We conclude that the KCNQ1 variant c.926C > T is the first identified LQTS-related founder mutation in Central Europe. The dominant negative channel dysfunction may lead to DADs under β-adrenergic stimulation. Inhibition of calcium current could be possible therapeutic strategy in LQTS1 patients refractory to β-blocker therapy.
Optimizing proton minibeam radiotherapy by interlacing and heterogeneous tumor dose on the basis of calculated clonogenic cell survival
Authors: Sammer Matthias , Girst Stefanie , Dollinger Günther 
Published: February 2021

AbstractProton minibeam radiotherapy (pMBRT) is a spatial fractionation method using sub-millimeter beams at center-to-center (ctc) distances of a few millimeters to widen the therapeutic index by reduction of side effects in normal tissues. Interlaced minibeams from two opposing or four orthogonal directions are calculated to minimize side effects. In particular, heterogeneous dose distributions applied to the tumor are investigated to evaluate optimized sparing capabilities of normal tissues at the close tumor surrounding. A 5 cm thick tumor is considered at 10 cm depth within a 25 cm thick water phantom. Pencil and planar minibeams are interlaced from two (opposing) directions as well as planar beams from four directions. An initial beam size of σ0 = 0.2 mm (standard deviation) is assumed in all cases. Tissue sparing potential is evaluated by calculating mean clonogenic cell survival using a linear-quadratic model on the calculated dose distributions. Interlacing proton minibeams for homogeneous irradiation of the tumor has only minor benefits for the mean clonogenic cell survival compared to unidirectional minibeam irradiation modes. Enhanced mean cell survival, however, is obtained when a heterogeneous dose distribution within the tumor is permitted. The benefits hold true even for an elevated mean tumor dose, which is necessary to avoid cold spots within the tumor in concerns of a prescribed dose. The heterogeneous irradiation of the tumor allows for larger ctc distances. Thus, a high mean cell survival of up to 47% is maintained even close to the tumor edges for single fraction doses in the tumor of at least 10 Gy. Similar benefits would result for heavy ion minibeams with the advantage of smaller minibeams in deep tissue potentially offering even increased tissue sparing. The enhanced mean clonogenic cell survival through large ctc distances for interlaced pMBRT with heterogeneous tumor dose distribution results in optimum tissue sparing potential. The calculations show the largest enhancement of the mean cell survival in normal tissue for high-dose fractions. Thus, hypo-fractionation or even single dose fractions become possible for tumor irradiation. A widened therapeutic index at big cost reductions is offered by interlaced proton or heavy ion minibeam therapy.
RNAseq shows an all-pervasive day-night rhythm in the transcriptome of the pacemaker of the heart
Authors: Wang Yanwen , Anderson Cali , Dobrzynski Halina , Hart George , D’Souza Alicia , Boyett Mark R. 
Published: February 2021

AbstractPhysiological systems vary in a day-night manner anticipating increased demand at a particular time. Heart is no exception. Cardiac output is primarily determined by heart rate and unsurprisingly this varies in a day-night manner and is higher during the day in the human (anticipating increased day-time demand). Although this is attributed to a day-night rhythm in post-translational ion channel regulation in the heart’s pacemaker, the sinus node, by the autonomic nervous system, we investigated whether there is a day-night rhythm in transcription. RNAseq revealed that ~ 44% of the sinus node transcriptome (7134 of 16,387 transcripts) has a significant day-night rhythm. The data revealed the oscillating components of an intrinsic circadian clock. Presumably this clock (or perhaps the master circadian clock in the suprachiasmatic nucleus) is responsible for the rhythm observed in the transcriptional machinery, which in turn is responsible for the rhythm observed in the transcriptome. For example, there is a rhythm in transcripts responsible for the two principal pacemaker mechanisms (membrane and Ca2+clocks), transcripts responsible for receptors and signalling pathways known to control pacemaking, transcripts from genes identified by GWAS as determinants of resting heart rate, and transcripts from genes responsible for familial and acquired sick sinus syndrome.
Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex
Authors: Ajjugal Yogeeshwar , Tomar Kripi , Rao D. Krishna , Rathinavelan Thenmalarchelvi 
Published: February 2021

AbstractBase pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.