bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduced hippocampal gray matter volume is a common feature of patients with major depression, bipolar disorder, and schizophrenia spectrum disorders
Authors: Brosch Katharina , Stein Frederike , Schmitt Simon , Pfarr Julia-Katharina , Ringwald Kai G. , Thomas-Odenthal Florian , Meller Tina , Steinsträter Olaf , Waltemate Lena , Lemke Hannah , Meinert Susanne , Winter Alexandra , Breuer Fabian , Thiel Katharina , Grotegerd Dominik , Hahn Tim , Jansen Andreas , Dannlowski Udo , Krug Axel , Nenadić Igor , Kircher Tilo
Published: July 2022

Major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia spectrum disorder (SSD, schizophrenia, and schizoaffective disorder) overlap in symptomatology, risk factors, genetics, and other biological measures. Based on previous findings, it remains unclear what transdiagnostic regional gray matter volume (GMV) alterations exist across these disorders, and with which factors they are associated. GMV (3-T magnetic resonance imaging) was compared between healthy controls (HC; n = 110), DSM-IV-TR diagnosed MDD (n = 110), BD (n = 110), and SSD patients (n = 110), matched for age and sex. We applied a conjunction analysis to identify shared GMV alterations across the disorders. To identify potential origins of identified GMV clusters, we associated them with early and current risk and protective factors, psychopathology, and neuropsychology, applying multiple regression models. Common to all diagnoses (vs. HC), we identified GMV reductions in the left hippocampus. This cluster was associated with the neuropsychology factor working memory/executive functioning, stressful life events, and with global assessment of functioning. Differential effects between groups were present in the left and right frontal operculae and left insula, with volume variances across groups highly overlapping. Our study is the first with a large, matched, transdiagnostic sample to yield shared GMV alterations in the left hippocampus across major mental disorders. The hippocampus is a major network hub, orchestrating a range of mental functions. Our findings underscore the need for a novel stratification of mental disorders, other than categorical diagnoses.
Low-dose post-transplant cyclophosphamide with low-dose antithymocyte globulin for prevention of graft-versus-host disease in first complete remission undergoing 10/10 HLA-matched unrelated donor peripheral blood stem cell transplants: a multicentre, randomized controlled trial
Authors: Zu Yingling , Li Zhen , Gui Ruirui , Liu Yanyan , Zhang Yanli , Yu Fengkuan , Zhao Huifang , Fu Yuewen , Zhan Xinrong , Wang Zhongliang , Xing Pengtao , Wang Xianjing , Wang Huili , Zhou Jian , Song Yongping
Published: July 2022

The most widely used regimens of graft-versus-host disease (GVHD) prophylaxis in HLA-matched unrelated donor peripheral blood stem cell transplantation (MUD-PBSCT) are based on anti-thymocyte globulin (ATG) or post-transplant cyclophosphamide (PTCy). To improve the efficiency of GVHD prophylaxis, a novel regimen, composed of low-dose PTCy (20 mg/kg on day +3 and +4) and low-dose ATG (6 mg/kg), was evaluted in patients with hematological malignancies ungoing 10/10 HLA MUD-PBSCT in first remission (CR1). In our prospective, multicenter study, 104 patients were randomly assigned one-to-one to low-dose PTCy-ATG (n = 53) or standard-dose ATG (10 mg/kg, n = 51). Both the cumulative incidences (CIs) of grade II-IV acute GVHD (aGVHD) and chronic GVHD (cGVHD) at 2 years in low-dose PTCy-ATG cohort were significantly reduced (24.5% vs. 47.1%; P = 0.017; 14.1% vs. 33.3%; P = 0.013). The CI of non-relapse-mortality (NRM) was much lower (13.2% vs. 34.5%; P = 0.049) and GVHD-free, relapse-free survival (GRFS) was significantly improved at 2 years in low-dose PTCy-ATG arm (67.3% vs 42.3%; P = 0.032). The low-dose PTCy-ATG based GVHD prophylaxis is a promising strategy for patients in CR1 after 10/10 HLA MUD-PBSCT.
Nrf2 overexpression increases the resistance of acute myeloid leukemia to cytarabine by inhibiting replication factor C4
Authors: Hu Tianzhen , Pan Chengyun , Zhang Tianzhuo , Ni Ming , Wang Weili , Zhang Siyu , Chen Ying , Wang Jishi , Fang Qin
Published: July 2022

Drug resistance is a key factor in the treatment failure of acute myeloid leukemia (AML). Nuclear factor E2-related factor 2 (Nrf2) plays a crucial role in tumor chemotherapy resistance. However, the potential mechanism of Nrf2 regulating DNA mismatch repair (MMR) pathway to mediate gene-instability drug resistance in AML is still unclear. Here, it was found that Nrf2 expression was closely related to the disease progression of AML as well as highly expressed in AML patients with poor prognostic gene mutations. Meanwhile, it was also found that the expression of Nrf2 was significantly negatively correlated with DNA MMR gene replication factor C4 (RFC4) in AML. CHIP analysis combined with luciferase reporter gene results further showed that Nrf2 may inhibit the expression of RFC4 by its interaction with the RFC4 promoter. In vitro and vivo experiments showed that the overexpression of Nrf2 decreased the killing effect of chemotherapy drug cytarabine (Ara-C) on leukemia cells and inhibited the expression of RFC4. Mechanistically, The result that Nrf2-RFC4 axis mediated AML genetic instability drug resistance might be received by activating the JNK/NF-κB signaling pathway. Taken together, these findings may provide a new idea for improving AML drug resistance.
TRAIL protects the immature lung from hyperoxic injury
Authors: Shahzad Tayyab , Chao Cho-Ming , Hadzic Stefan , Behnke Judith , Biebach Luisa , Böttcher-Friebertshäuser Eva , Wilhelm Jochen , Hilgendorff Anne , Zimmer Klaus-Peter , Morty Rory E. , Bellusci Saverio , Ehrhardt Harald
Published: July 2022

The hyperoxia-induced pro-inflammatory response and tissue damage constitute pivotal steps leading to bronchopulmonary dysplasia (BPD) in the immature lung. The pro-inflammatory cytokines are considered attractive candidates for a directed intervention but the complex interplay between inflammatory and developmental signaling pathways requires a comprehensive evaluation before introduction into clinical trials as studied here for the death inducing ligand TRAIL. At birth and during prolonged exposure to oxygen and mechanical ventilation, levels of TRAIL were lower in tracheal aspirates of preterm infants <29 weeks of gestation which developed moderate/severe BPD. These findings were reproduced in the newborn mouse model of hyperoxic injury. The loss of TRAIL was associated with increased inflammation, apoptosis induction and more pronounced lung structural simplification after hyperoxia exposure for 7 days while activation of NFκB signaling during exposure to hyperoxia was abrogated. Pretreatment with recombinant TRAIL rescued the developmental distortions in precision cut lung slices of both wildtype and TRAIL−/− mice exposed to hyperoxia. Of importance, TRAIL preserved alveolar type II cells, mesenchymal progenitor cells and vascular endothelial cells. In the situation of TRAIL depletion, our data ascribe oxygen toxicity a more injurious impact on structural lung development. These data are not surprising taking into account the diverse functions of TRAIL and its stimulatory effects on NFκB signaling as central driver of survival and development. TRAIL exerts a protective role in the immature lung as observed for the death inducing ligand TNF-α before.
Glutamate drives ‘local Ca2+ release’ in cardiac pacemaker cells
Authors: Xie Duanyang , Xiong Ke , Su Xuling , Wang Guanghua , Zou Qicheng , Wang Luxin , Zhang Caihong , Cao Yuting , Shao Beihua , Zhang Yixin , Zhang Peidong , Liang Dandan , Liu Yi , Chen Yi-Han
Published: July 2022

The sinoatrial node (SAN) is the origin of the electrical signals for rhythmic heartbeats in mammals. The spontaneous firing of SAN pacemaker cells (SANPCs) triggers cardiac contraction. ‘Local Ca2+ release’ (LCR), a unique cellular activity, acts as the ‘engine’ of the spontaneous firing of SANPCs. However, the mechanism of LCR initiation remains unclear. Here, we report that endogenous glutamate drives LCRs in SANPCs. Using a glutamate sensor, we unraveled a tight correlation between glutamate accumulation and LCR occurrence, indicating a potential relationship between glutamate and LCRs. Intracellular application of glutamate significantly enhanced the LCRs in both intact and permeabilized SANPCs. Mechanistically, we revealed that mitochondrial excitatory amino acid transporter 1 (EAAT1)-dependent mitochondrial glutamate import promoted ROS generation, which in turn led to the oxidation of Ca2+-handling proteins, ultimately resulting in enhanced LCRs. Importantly, EAAT1 depletion reduced both the spontaneous firing rates of isolated SANPCs and the heart rate in vitro and in vivo, suggesting the central role of EAAT1 as a glutamate transporter in the regulation of cardiac autonomic rhythm. In conclusion, our results indicate that glutamate serves as an LCR igniter in SANPCs, adding a potentially important element to the coupled-clock theory that explains the origin of spontaneous firing. These findings shed new light on the future prevention and treatment of cardiac pacemaker cell-related arrhythmias.
Quantifying interactions on interfaces between metal particles and oxide supports in catalytic nanomaterials
Authors: Neyman Konstantin M. , Kozlov Sergey M.
Published: July 2022

Metal-support interactions can dramatically affect the properties of nanocomposite materials. Nevertheless, comprehensive studies of the interfaces between metal nanoparticles and oxide supports remain scarce due to challenges in experimental characterization. A significant understanding of the interactions at such interfaces can be obtained by combining state-of-the-art experiments with density functional calculations. In particular, this Perspective illustrates how theory and experiment can be combined to study interfacial charge transfer, the short- or long-range natures of nanoparticle-support interactions and the effects of oxide nanostructuring on the properties of supported metal particles. These studies aid our understanding of the role of metal-oxide interactions in industrially employed nanocomposites and the design of interfaces with unique properties for future applications.
The Medical Segmentation Decathlon
Authors: Antonelli Michela , Reinke Annika , Bakas Spyridon , Farahani Keyvan , Kopp-Schneider Annette , Landman Bennett A. , Litjens Geert , Menze Bjoern , Ronneberger Olaf , Summers Ronald M. , van Ginneken Bram , Bilello Michel , Bilic Patrick , Christ Patrick F. , Do Richard K. G. , Gollub Marc J. , Heckers Stephan H. , Huisman Henkjan , Jarnagin William R. , McHugo Maureen K. , Napel Sandy , Pernicka Jennifer S. Golia , Rhode Kawal , Tobon-Gomez Catalina , Vorontsov Eugene , Meakin James A. , Ourselin Sebastien , Wiesenfarth Manuel , Arbeláez Pablo , Bae Byeonguk , Chen Sihong , Daza Laura , Feng Jianjiang , He Baochun , Isensee Fabian , Ji Yuanfeng , Jia Fucang , Kim Ildoo , Maier-Hein Klaus , Merhof Dorit , Pai Akshay , Park Beomhee , Perslev Mathias , Rezaiifar Ramin , Rippel Oliver , Sarasua Ignacio , Shen Wei , Son Jaemin , Wachinger Christian , Wang Liansheng , Wang Yan , Xia Yingda , Xu Daguang , Xu Zhanwei , Zheng Yefeng , Simpson Amber L. , Maier-Hein Lena , Cardoso M. Jorge
Published: July 2022

International challenges have become the de facto standard for comparative assessment of image analysis algorithms. Although segmentation is the most widely investigated medical image processing task, the various challenges have been organized to focus only on specific clinical tasks. We organized the Medical Segmentation Decathlon (MSD)—a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities to investigate the hypothesis that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. MSD results confirmed this hypothesis, moreover, MSD winner continued generalizing well to a wide range of other clinical problems for the next two years. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to scientists that are not versed in AI model training.
Trigger factor both holds and folds its client proteins
Authors: Wu Kevin , Minshull Thomas C. , Radford Sheena E. , Calabrese Antonio N. , Bardwell James C. A.
Published: July 2022

ATP-independent chaperones like trigger factor are generally assumed to play passive roles in protein folding by acting as holding chaperones. Here we show that trigger factor plays a more active role. Consistent with a role as an aggregation inhibiting chaperone, we find that trigger factor rapidly binds to partially folded glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prevents it from non-productive self-association by shielding oligomeric interfaces. In the traditional view of holding chaperone action, trigger factor would then be expected to transfer its client to a chaperone foldase system for complete folding. Unexpectedly, we noticed that GAPDH folds into a monomeric but otherwise rather native-like intermediate state while trigger factor-bound. Upon release from trigger factor, the mostly folded monomeric GAPDH rapidly self-associates into its native tetramer and acquires enzymatic activity without needing additional folding factors. The mechanism we propose here for trigger factor bridges the holding and folding activities of chaperone function.
Constrained CMIP6 projections indicate less warming and a slower increase in water availability across Asia
Authors: Chai Yuanfang , Yue Yao , Slater Louise J. , Yin Jiabo , Borthwick Alistair G. L. , Chen Tiexi , Wang Guojie
Published: July 2022

Climate projections are essential for decision-making but contain non-negligible uncertainty. To reduce projection uncertainty over Asia, where half the world’s population resides, we develop emergent constraint relationships between simulated temperature (1970–2014) and precipitation (2015–2100) growth rates using 27 CMIP6 models under four Shared Socioeconomic Pathways. Here we show that, with uncertainty successfully narrowed by 12.1–31.0%, constrained future precipitation growth rates are 0.39 ± 0.18 mm year−1 (29.36 mm °C−1, SSP126), 0.70 ± 0.22 mm year−1 (20.03 mm °C−1, SSP245), 1.10 ± 0.33 mm year−1 (17.96 mm °C−1, SSP370) and 1.42 ± 0.35 mm year−1 (17.28 mm °C−1, SSP585), indicating overestimates of 6.0–14.0% by the raw CMIP6 models. Accordingly, future temperature and total evaporation growth rates are also overestimated by 3.4–11.6% and −2.1–13.0%, respectively. The slower warming implies a lower snow cover loss rate by 10.5–40.2%. Overall, we find the projected increase in future water availability is overestimated by CMIP6 over Asia.
Hepatic non-parenchymal S100A9-TLR4-mTORC1 axis normalizes diabetic ketogenesis
Authors: Ursino Gloria , Ramadori Giorgio , Höfler Anna , Odouard Soline , Teixeira Pryscila D. S. , Visentin Florian , Veyrat-Durebex Christelle , Lucibello Giulia , Firnkes Raquel , Ricci Serena , Vianna Claudia R. , Jia Lin , Dirlewanger Mirjam , Klee Philippe , Elmquist Joel K. , Roth Johannes , Vogl Thomas , Schwitzgebel Valérie M. , Jornayvaz François R. , Boland Andreas , Coppari Roberto
Published: July 2022

Unrestrained ketogenesis leads to life-threatening ketoacidosis whose incidence is high in patients with diabetes. While insulin therapy reduces ketogenesis this approach is sub-optimal. Here, we report an insulin-independent pathway able to normalize diabetic ketogenesis. By generating insulin deficient male mice lacking or re-expressing Toll-Like Receptor 4 (TLR4) only in liver or hepatocytes, we demonstrate that hepatic TLR4 in non-parenchymal cells mediates the ketogenesis-suppressing action of S100A9. Mechanistically, S100A9 acts extracellularly to activate the mechanistic target of rapamycin complex 1 (mTORC1) in a TLR4-dependent manner. Accordingly, hepatic-restricted but not hepatocyte-restricted loss of Tuberous Sclerosis Complex 1 (TSC1, an mTORC1 inhibitor) corrects insulin-deficiency-induced hyperketonemia. Therapeutically, recombinant S100A9 administration restrains ketogenesis and improves hyperglycemia without causing hypoglycemia in diabetic mice. Also, circulating S100A9 in patients with ketoacidosis is only marginally increased hence unveiling a window of opportunity to pharmacologically augment S100A9 for preventing unrestrained ketogenesis. In summary, our findings reveal the hepatic S100A9-TLR4-mTORC1 axis in non-parenchymal cells as a promising therapeutic target for restraining diabetic ketogenesis.
The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance
Authors: Ferguson Ian D. , Patiño-Escobar Bonell , Tuomivaara Sami T. , Lin Yu-Hsiu T. , Nix Matthew A. , Leung Kevin K. , Kasap Corynn , Ramos Emilio , Nieves Vasquez Wilson , Talbot Alexis , Hale Martina , Naik Akul , Kishishita Audrey , Choudhry Priya , Lopez-Girona Antonia , Miao Weili , Wong Sandy W. , Wolf Jeffrey L. , Martin Thomas G. , Shah Nina , Vandenberg Scott , Prakash Sonam , Besse Lenka , Driessen Christoph , Posey Avery D. , Mullins R. Dyche , Eyquem Justin , Wells James A. , Wiita Arun P.
Published: July 2022

The myeloma surface proteome (surfaceome) determines tumor interaction with the microenvironment and serves as an emerging arena for therapeutic development. Here, we use glycoprotein capture proteomics to define the myeloma surfaceome at baseline, in drug resistance, and in response to acute drug treatment. We provide a scoring system for surface antigens and identify CCR10 as a promising target in this disease expressed widely on malignant plasma cells. We engineer proof-of-principle chimeric antigen receptor (CAR) T-cells targeting CCR10 using its natural ligand CCL27. In myeloma models we identify proteins that could serve as markers of resistance to bortezomib and lenalidomide, including CD53, CD10, EVI2B, and CD33. We find that acute lenalidomide treatment increases activity of MUC1-targeting CAR-T cells through antigen upregulation. Finally, we develop a miniaturized surface proteomic protocol for profiling primary plasma cell samples with low inputs. These approaches and datasets may contribute to the biological, therapeutic, and diagnostic understanding of myeloma.
Inhibition of NMDA receptors through a membrane-to-channel path
Authors: Wilcox Madeleine R. , Nigam Aparna , Glasgow Nathan G. , Narangoda Chamali , Phillips Matthew B. , Patel Dhilon S. , Mesbahi-Vasey Samaneh , Turcu Andreea L. , Vázquez Santiago , Kurnikova Maria G. , Johnson Jon W.
Published: July 2022

N-methyl-d-aspartate receptors (NMDARs) are transmembrane proteins that are activated by the neurotransmitter glutamate and are found at most excitatory vertebrate synapses. NMDAR channel blockers, an antagonist class of broad pharmacological and clinical significance, inhibit by occluding the NMDAR ion channel. A vast literature demonstrates that NMDAR channel blockers, including MK-801, phencyclidine, ketamine, and the Alzheimer’s disease drug memantine, can bind and unbind only when the NMDAR channel is open. Here we use electrophysiological recordings from transfected tsA201 cells and cultured neurons, NMDAR structural modeling, and custom-synthesized compounds to show that NMDAR channel blockers can enter the channel through two routes: the well-known hydrophilic path from extracellular solution to channel through the open channel gate, and also a hydrophobic path from plasma membrane to channel through a gated fenestration (“membrane-to-channel inhibition” (MCI)). Our demonstration that ligand-gated channels are subject to MCI, as are voltage-gated channels, highlights the broad expression of this inhibitory mechanism.
Post-recovery COVID-19 and incident heart failure in the National COVID Cohort Collaborative (N3C) study
Authors: Salah Husam M. , Fudim Marat , O’Neil Shawn T. , Manna Amin , Chute Christopher G. , Caughey Melissa C.
Published: July 2022

Cardiac involvement has been noted in COVID-19 infection. However, the relationship between post-recovery COVID-19 and development of de novo heart failure has not been investigated in a large, nationally representative population. We examined post-recovery outcomes of 587,330 patients hospitalized in the United States (257,075 with COVID-19 and 330,255 without), using data from the National COVID Cohort Collaborative study. Patients hospitalized with COVID-19 were older (51 vs. 46 years), more often male (49% vs. 42%), and less often White (61% vs. 69%). Over a median follow up of 367 days, 10,979 incident heart failure events occurred. After adjustments, COVID-19 hospitalization was associated with a 45% higher hazard of incident heart failure (hazard ratio = 1.45; 95% confidence interval: 1.39–1.51), with more pronounced associations among patients who were younger (P-interaction = 0.003), White (P-interaction = 0.005), or who had established cardiovascular disease (P-interaction = 0.005). In conclusion, COVID-19 hospitalization is associated with increased risk of incident heart failure.
Fermi surface tomography
Authors: Borisenko Sergey , Fedorov Alexander , Kuibarov Andrii , Bianchi Marco , Bezguba Volodymyr , Majchrzak Paulina , Hofmann Philip , Baumgärtel Peter , Voroshnin Vladimir , Kushnirenko Yevhen , Sánchez-Barriga Jaime , Varykhalov Andrei , Ovsyannikov Ruslan , Morozov Igor , Aswartham Saicharan , Feia Oleh , Harnagea Luminita , Wurmehl Sabine , Kordyuk Alexander , Yaresko Alexander , Berger Helmuth , Büchner Bernd
Published: July 2022

Fermi surfaces are essential for predicting, characterizing and controlling the properties of crystalline metals and semiconductors. Angle-resolved photoemission spectroscopy (ARPES) is the only technique directly probing the Fermi surface by measuring the Fermi momenta (kF) from energy- and angular distribution of photoelectrons dislodged by monochromatic light. Existing apparatus is able to determine a number of kF -vectors simultaneously, but direct high-resolution 3D Fermi surface mapping remains problematic. As a result, no such datasets exist, strongly limiting our knowledge about the Fermi surfaces. Here we show that using a simpler instrumentation it is possible to perform 3D-mapping within a very short time interval and with very high resolution. We present the first detailed experimental 3D Fermi surface as well as other experimental results featuring advantages of our technique. In combination with various light sources our methodology and instrumentation offer new opportunities for high-resolution ARPES in the physical and life sciences.
Humanized mice for investigating sustained Plasmodium vivax blood-stage infections and transmission
Authors: Luiza-Batista Camilla , Thiberge Sabine , Serra-Hassoun Malika , Nardella Flore , Claës Aurélie , Nicolete Vanessa C. , Commère Pierre-Henri , Mancio-Silva Liliana , Ferreira Marcelo U. , Scherf Artur , Garcia Sylvie
Published: July 2022

Plasmodium vivax is the most widespread human malaria parasite. Due to the presence of extravascular reservoirs and relapsing infections from dormant liver stages, P. vivax is particularly difficult to control and eliminate. Experimental research is hampered by the inability to maintain P. vivax cultures in vitro, due to its tropism for immature red blood cells (RBCs). Here, we describe a new humanized mice model that can support efficient human erythropoiesis and maintain long-lasting multiplication of inoculated cryopreserved P. vivax parasites and their sexual differentiation, including in bone marrow. Mature gametocytes were transmitted to Anopheles mosquitoes, which led to the formation of salivary gland sporozoites. Importantly, blood-stage P. vivax parasites were maintained after the secondary transfer of fresh or frozen infected bone marrow cells to naïve chimeras. This model provides a unique tool for investigating, in vivo, the biology of intraerythrocytic P. vivax.
Responding to eruptive transitions during the 2020–2021 eruption of La Soufrière volcano, St. Vincent
Authors: Joseph E. P. , Camejo-Harry M. , Christopher T. , Contreras-Arratia R. , Edwards S. , Graham O. , Johnson M. , Juman A. , Latchman J. L. , Lynch L. , Miller V. L. , Papadopoulos I. , Pascal K. , Robertson R. , Ryan G. A. , Stinton A. , Grandin R. , Hamling I. , Jo M-J. , Barclay J. , Cole P. , Davies B. V. , Sparks R. S. J.
Published: July 2022

A critical challenge during volcanic emergencies is responding to rapid changes in eruptive behaviour. Actionable advice, essential in times of rising uncertainty, demands the rapid synthesis and communication of multiple datasets with prognoses. The 2020–2021 eruption of La Soufrière volcano exemplifies these challenges: a series of explosions from 9–22 April 2021 was preceded by three months of effusive activity, which commenced with a remarkably low level of detected unrest. Here we show how the development of an evolving conceptual model, and the expression of uncertainties via both elicitation and scenarios associated with this model, were key to anticipating this transition. This not only required input from multiple monitoring datasets but contextualisation via state-of-the-art hazard assessments, and evidence-based knowledge of critical decision-making timescales and community needs. In addition, we share strategies employed as a consequence of constraints on recognising and responding to eruptive transitions in a resource-constrained setting, which may guide similarly challenged volcano observatories worldwide.
A chromosome-level genome assembly of the jade perch (Scortum barcoo)
Authors: Lu Yishan , Li Ruihan , Xia Liqun , Cheng Jun , Xia Hongli , Zhan Qiuyao , Yu Dapeng , You Xinxin , Gu Ruobo , Xu Junmin , Shi Qiong , Bian Chao
Published: July 2022

Endemic to Australia, jade perch (Scortum barcoo) is a highly profitable freshwater bass species. It has extraordinarily high levels of omega-3 polyunsaturated fatty acids (PUFAs), which detailed genes involved in are largely unclear. Meanwhile, there were four chromosome-level bass species have been previous sequenced, while the bass ancestor genome karyotypes have not been estimated. Therefore, we sequenced, assembled and annotated a genome of jade perch to characterize the detailed genes for biosynthesis of omega-3 PUFAs and to deduce the bass ancestor genome karyotypes. We constructed a chromosome-level genome assembly with 24 pairs of chromosomes, 657.7 Mb in total length, and the contig and the scaffold N50 of 4.8 Mb and 28.6 Mb respectively. We also identified repetitive elements (accounting for 19.7% of the genome assembly) and predicted 26,905 protein-coding genes. Meanwhile, we performed genome-wide localization and characterization of several important genes encoding some key enzymes in the biosynthesis pathway of PUFAs. These genes may contribute to the high concentration of omega-3 in jade perch. Moreover, we conducted a series of comparative genomic analyses among four representative bass species at a chromosome level, resulting in a series of sequences of a deductive bass ancestor genome.
The draft genome sequence of the Brahminy blindsnake Indotyphlops braminus
Authors: Khedkar Gulab , Kambayashi Chiaki , Tabata Hiromasa , Takemura Ikuyo , Minei Ryuhei , Ogura Atsushi , Kurabayashi Atsushi
Published: July 2022

Blindsnakes of infraoder Scolecophidia (order Squamata) are the most basal group of extant snakes, comprising of more than 450 species with ecological and morphological features highly specialized to underground living. The Brahminy blindsnake, Indotyphlops braminus, is the only known obligate parthenogenetic species of snakes. Although the origin of I. braminus is thought to be South Asia, this snake has attracted worldwide attention as an alien species, as it has been introduced to all continents except Antarctica. In this study, we present the first draft genome assembly and annotation of I. braminus. We generated approximately 480 Gbp of sequencing data and produced a draft genome with a total length of 1.86 Gbp and N50 scaffold size of 1.25 Mbp containing 89.3% of orthologs conserved in Sauropsida. We also identified 0.98 Gbp (52.82%) of repetitive genome sequences and a total of 23,560 protein-coding genes. The first draft genome of I. braminus will facilitate further study of snake evolution as well as help to understand the emergence mechanism of parthenogenetic vertebrates.
On solving the chlorine transport model via Laplace transform
Authors: Aljohani A. F. , Ebaid A. , Algehyne E. A. , Mahrous Y. M. , Agarwal P. , Areshi M. , Al-Jeaid H. K.
Published: July 2022

This paper analyzes the two-dimensional chlorine-transport model in pipes. The studied model is in the form of a second-order partial differential equation with a set of boundary conditions. Obtaining exact solution for the current model is a challenge due to the nature of the involved boundary conditions, especially, when applying the Laplace transform. However, such difficulties are solved via implementing the method of residues. The exact solution is obtained in terms of the Bessel functions. The expression for a dimensionless cup-mixing average concentration is also derived analytically. The proposed approach is validated via numerical examples for comparing the results with those in the literature. The present analysis/approach is effective/straightforward and can be further applied on other similar models under different boundary conditions.
Contralateral patent processus vaginalis repair in boys: a single-center retrospective study
Authors: Jinxiang Liu , Qingwei Cao , Shenghua Qiu , Yunqiang Xia , Haiyang Liu , Chengliang Liu , Meng Xu
Published: July 2022

To ascertain the prevalence of contralateral patent processus vaginalis (CPPV) in life and the significance of the prevalence trends for treatment. We performed a retrospective review of all inguinal hernias (IHs) that underwent repair in our hospital from 2014 to 2018. We analyzed the frequency of occurrence and treatment in boys. We assessed and compared the history, initial sides of hernia, CPPV and prognoses in different age groups. We assessed all IH cases repaired in our hospital and selected male patients of a variety of ages, including boys and men. Recurrent cases were not enrolled. A total of 3243 cases were enrolled: 2489 [right-sided IH 1411 (56.69%) vs. left-sided IH 975 (39.17%), bilateral IH 103 (4.14%)] in children and 754 [right-sided IH 485 (64.32%) vs. left-sided IH 236 (31.30%), bilateral IH 33 (4.38%)] in adults. A total of 1124 CPPVs were identified in children with unilateral IH (2386), and 12 were identified in adults (267) (p < 0.0001). There were no significant differences in recurrence rate between different subgroups of children (p > 0.05). The incidence of IH in boys was significantly higher than that in men. The number of incident cases declines rapidly with age in boys. The processus vaginalis is normally obliterated and involuted but may instead remain patent for a long period before closure; routine exploration on the contralateral side may eliminate the possibility of spontaneous PPV closure.
Uric acid and cardiometabolic risk by gender in youth with type 1 diabetes
Authors: Di Bonito Procolo , Rosanio Francesco Maria , Marcovecchio Maria Loredana , Cherubini Valentino , Delvecchio Maurizio , Di Candia Francesca , Iafusco Dario , Zanfardino Angela , Iovane Brunella , Maffeis Claudio , Maltoni Giulio , Ripoli Carlo , Piccinno Elvira , Piona Claudia Anita , Ricciardi Maria Rossella , Schiaffini Riccardo , Franzese Adriana , Mozzillo Enza
Published: July 2022

The aim of this study was to investigate the association between uric acid (UA) and cardiometabolic risk factors (CMRFs) by sex in youth with type 1 diabetes (T1D). Retrospective data collected from 1323 children and adolescents (5–18 years; 716 boys) with T1D recruited in 9 Italian Pediatric Diabetes Centers were analyzed. CMRFs included UA, HbA1c, blood pressure (BP), cholesterol (TC), HDL, triglycerides (TG), neutrophils (N) and lymphocytes (L) count, glomerular filtration rate (eGFR) (calculated using Schwartz-Lyon equation). In boys, we found a higher age, daily insulin dose, TG, TG/HDL ratio, TC/HDL ratio, systolic BP, N/L ratio and lower HDL, and eGFR across UA tertiles (p = 0.01–0.0001). Similar results were found in girls but not for TG and systolic BP. In boys, the odds ratio (OR) of high levels of TG/HDL ratio, TC/HDL ratio, BP and mildly reduced eGFR (MRGFR) increased for 0.5 mg/dL of UA. Instead, in girls an increased levels of 0.5 mg/dL of UA were associated with high OR of TC/HDL ratio, N/L ratio and MRGFR. Uric acid may represent a useful marker for identifying youth with T1D at high cardiometabolic risk, and this association appears to vary by sex.
Antioxidant, cytotoxic and apoptotic activities of the rhizome of Zingiber zerumbet Linn. in Ehrlich ascites carcinoma bearing Swiss albino mice
Authors: Ali Hanif , Hasi Rumana Yesmin , Islam Majidul , Haque Md Shajedul , Alkhanani Mustfa F. , Almalki Atiah H. , Haque Shafiul , Sayyed R. Z. , Yeasmin Tanzima
Published: July 2022

Due to having a long history of traditional uses as a functional food, Zingiber zerumbet was selected here to explore the inherent antioxidant and antineoplastic activities of methanolic extract of its rhizome (MEZZR) against Ehrlich ascites carcinoma (EAC) cells. The rich polyphenol containing MEZZR showed a marked DPPH, ABTS, nitric oxide radicals and lipid peroxidation inhibition activity with an IC50 of 3.43 ± 1.25, 11.38 ± 1.39, 23.12 ± 3.39 and 16.47 ± 1.47 µg/ml, respectively, when compared to the standard catechin. In vivo, MEZZR significantly inhibited EAC cell growth, decreased body weight gain, increased life span and restored the altered hematological characteristics of EAC-bearing mice. Moreover, MEZZR induced nuclear condensation and fragmentation, which are notable features of apoptosis as observed by fluorescence microscopy after staining EAC cells of MEZZR-treated mice with Hoechst 33342. Additionally, in vitro, the cell growth inhibition caused by the MEZZR in MTT assay, was remarkably decreased in the presence of caspase-3, -8 and -9 inhibitors. This study thus suggests that MEZZR may possess promising antiproliferative efficacy against EAC cells by inducing cell apoptosis.
Applying fluorescent dye assays to discriminate Escherichia coli chlorhexidine resistance phenotypes from porin and mlaA deletions and efflux pumps
Authors: Gregorchuk Branden S. J. , Reimer Shelby L. , Slipski Carmine J. , Milner Kieran A. , Hiebert Shannon L. , Beniac Daniel R. , Booth Timothy F. , Zhanel George G. , Bay Denice C.
Published: July 2022

Bacterial resistance to the antiseptic chlorhexidine (CHX), is a growing problem, recently shown to be caused by deleterious mutations to the phospholipid transport system component (mlaA) as well as efflux pump overexpression. Comparisons of CHX resistance mechanisms, such as porin deletions (ompCF), and over-expressed efflux pumps (acrB, qacE, aceI), are lacking and may be distinguishable using antiseptic rapid fluorescent dye testing assays. Using E. coli K-12 CHX adapted isolates (CHXR1), gene deletion mutants, and over-expressed transformants the phenotypes of these CHX resistance genes were compared using antimicrobial susceptibility tests (AST), rapid fluorescent propidium iodide dye-based membrane integrity assays (RFDMIA), and scanning electron microscopy (SEM). AST findings showed CHXR1, ΔacrB, ΔompCF, and transformants pCA24N-aceI and pCA24N-mlaA conferred greater (two to fourfold) MIC changes when compared to matched controls. Examination of these mutants/transformants using CHX RFDMIA showed that porin dual-deletions (ΔompCF) and mlaA alterations (ΔmlaA; pCA24N-mlaA, CHXR1) were distinguishable from controls. Results for over-expressed (pMS119EH-aceI) and deleted (ΔacrB) efflux pump RFDMIA could not be distinguished with propidium iodide, only with ethidium bromide, suggesting propidium iodide is better suited for detecting porin and mlaA associated CHX resistance mechanisms. SEM of CHXR1 and unadapted E. coli cells exposed to increasing CHX concentrations revealed that CHX does not visibly damage cell envelope integrity at any tested concentration but did identify elongated CHXR1 cells. ΔmlaA confers similar levels of CHX resistance as efflux overexpression and porin deletions, however, only outer membrane-altering porin and mlaA deletions can be reliably distinguished using RFDMIA.
Pseudo-capacitive and kinetic enhancement of metal oxides and pillared graphite composite for stabilizing battery anodes
Authors: Luo Yongguang , Wang Lingling , Li Qian , Choi Jungsue , Park G. Hwan , Zheng Zhiyong , Liu Yang , Wang Hongdan , Lee Hyoyoung
Published: July 2022

Nanostructured TiO2and SnO2possess reciprocal energy storage properties, but challenges remain in fully exploiting their complementary merits. Here, this study reports a strategy of chemically suturing metal oxides in a cushioning graphite network (SnO2[O]rTiO2-PGN) in order to construct an advanced and reliable energy storage material with a unique configuration for energy storage processes. The suggested SnO2[O]rTiO2-PGN configuration provides sturdy interconnections between phases and chemically wraps the SnO2nanoparticles around disordered TiO2(SnO2[O]rTiO2) into a cushioning plier-linked graphite network (PGN) system with nanometer interlayer distance (~ 1.2 nm). Subsequently, the SnO2[O]rTiO2-PGN reveals superior lithium-ion storage performance compared to all 16 of the control group samples and commercial graphite anode (keeps around 600 mAh g−1at 100 mA g−1after 250 cycles). This work clarifies the enhanced pseudo-capacitive contribution and the major diffusion-controlled energy storage kinetics. The validity of preventing volume expansion is demonstrated through the visualized image evidence of electrode integrity.
MIL-125-based nanocarrier decorated with Palladium complex for targeted drug delivery
Authors: Bagherzadeh Mojtaba , Safarkhani Moein , Kiani Mahsa , Radmanesh Fatemeh , Daneshgar Hossein , Ghadiri Amir Mohammad , Taghavimandi Fahimeh , Fatahi Yousef , Safari-Alighiarloo Nahid , Ahmadi Sepideh , Rabiee Navid
Published: July 2022

The aim of this work was to provide a novel approach to designing and synthesizing a nanocomposite with significant biocompatibility, biodegradability, and stability in biological microenvironments. Hence, the porous ultra-low-density materials, metal–organic frameworks (MOFs), have been considered and the MIL-125(Ti) has been chosen due to its distinctive characteristics such as great biocompatibility and good biodegradability immobilized on the surface of the reduced graphene oxide (rGO). Based on the results, the presence of transition metal complexes next to the drug not only can reinforce the stability of the drug on the structure by preparing π–π interaction between ligands and the drug but also can enhance the efficiency of the drug by preventing the spontaneous release. The effect of utilizing transition metal complex beside drug (Doxorubicin (DOX)) on the drug loading, drug release, and antibacterial activity of prepared nanocomposites on the P. aeruginosa and S. aureus as a model bacterium has been investigated and the results revealed that this theory leads to increasing about 200% in antibacterial activity. In addition, uptake, the release of the drug, and relative cell viabilities (in vitro and in vivo) of prepared nanomaterials and biomaterials have been discussed. Based on collected data, the median size of prepared nanocomposites was 156.2 nm, and their biological stability in PBS and DMEM + 10% FBS was screened and revealed that after 2.880 min, the nanocomposite’s size reached 242.3 and 516 nm respectively. The MTT results demonstrated that immobilizing PdL beside DOX leads to an increase of more than 15% in the cell viability. It is noticeable that the AST:ALT result of prepared nanocomposite was under 1.5.
Progression detection capabilities of circumpapillary and macular vessel density in advanced glaucomatous eyes
Authors: Lee Anna , Sung Kyung Rim , Shin Joong Won
Published: July 2022

This study investigated the progression detection capabilities of circumpapillary and macular vessel density (cpVD and mVD) in advanced primary open angle glaucoma (POAG) eyes using the rates of change in VD (trend-based analysis) and variability limits derived from healthy eyes. (event-based analysis) This study included 75 POAG eyes [visual field (VF) mean deviation < − 10 decibels, mean follow-up; 2.3 years] and 33 healthy eyes. Of 75 POAG eyes, 17 (22.7 %) and 58 eyes (77.3 %) were classified into the VF progression and stable groups, respectively. The VF progression group showed significantly faster VD loss than the stable group. (cpVD; − 1.76 vs. − 0.84 %/year, mVD; − 1.10 vs. − 0.47 %/year, P < 0.05) However, the rates of change in circumpapillary retinal nerve fiber layer and macular ganglion cell complex thickness were similar between the groups. (cpRNFLT; − 0.67 vs. − 0.53 $$\mu$$
μ
m/year, GCCT; − 0.48 vs. − 0.12 $$\mu$$
μ
m/year, P > 0.05) Event-based analysis showed stronger agreement between VD and VF progression (cpVD; kappa value (k) = 0.630, mVD; k = 0.667, P < 0.05) than that between structure and VF progression. (cpRNFLT; k = 0.111, GCCT; k = 0.194, P > 0.05). In conclusion, VD loss showed better progression detection capabilities than structural loss in advanced POAG eyes. Detection of cpVD and mVD loss may be useful for detecting progression in the advanced stages of POAG to complement other reference standard strategies.
Subtercola endophyticus sp. nov., a cold-adapted bacterium isolated from Abies koreana
Authors: Jiang Lingmin , Peng Yuxin , Seo Jiyoon , Jeon Doeun , Jo Mi Gyeong , Lee Ju Huck , Jeong Jae Cheol , Kim Cha Young , Park Hyeong Cheol , Lee Jiyoung
Published: July 2022

A novel Gram-stain-positive, aerobic bacterial strain, designated AK-R2A1-2 T, was isolated from the surface-sterilized needle leaves of an Abies koreana tree. Strain AK-R2A1-2 T had 97.3% and 96.7% 16S rRNA gene sequence similarities with Subtercola boreus K300T and Subtercola lobariae 9583bT, respectively, but formed a distinct phyletic lineage from these two strains. Growth of strain AK-R2A1-2 T was observed at 4–25 °C at pH 5.0–8.0. Strain AK-R2A1-2 T contained menaquinone 9 (MK-9) and menaquinone 10 (MK-10) as the predominant respiratory quinones. The major cellular fatty acids were anteiso-C15:0 and summed feature 8 (C18:1ω7c or/and C18:1ω6c), and the polar lipids included diphosphatidylglycerol (DPG) and three unknown aminolipids, AKL2, AKL3, and AKL4. The complete genome of strain AK-R2A1-2 T was sequenced to understand the genetic basis of its survival at low temperatures. Multiple copies of cold-associated genes involved in cold-active chaperon, stress response, and DNA repair supported survival of the strain at low temperatures. Strain AK-R2A1-2 T was also able to significantly improve rice seedling growth under low temperatures. Thus, this strain represents a novel species of the genus Subtercola, and the proposed name is Subtercola endophyticus sp. nov. The type strain is AK-R2A1-2 T (= KCTC 49721 T = GDMCC 1.2921 T).
IHACRES, GR4J and MISD-based multi conceptual-machine learning approach for rainfall-runoff modeling
Authors: Mohammadi Babak , Safari Mir Jafar Sadegh , Vazifehkhah Saeed
Published: July 2022

As a complex hydrological problem, rainfall-runoff (RR) modeling is of importance in runoff studies, water supply, irrigation issues, and environmental management. Among the variety of approaches for RR modeling, conceptual approaches use physical concepts and are appropriate methods for representation of the physics of the problem while may fail in competition with their advanced alternatives. Contrarily, machine learning approaches for RR modeling provide high computation ability however, they are based on the data characteristics and the physics of the problem cannot be completely understood. For the sake of overcoming the aforementioned deficiencies, this study coupled conceptual and machine learning approaches to establish a robust and more reliable RR model. To this end, three hydrological process-based models namely: IHACRES, GR4J, and MISD are applied for runoff simulating in a snow-covered basin in Switzerland and then, conceptual models’ outcomes together with more hydro-meteorological variables were incorporated into the model structure to construct multilayer perceptron (MLP) and support vector machine (SVM) models. At the final stage of the modeling procedure, the data fusion machine learning approach was implemented through using the outcomes of MLP and SVM models to develop two evolutionary models of fusion MLP and hybrid MLP-whale optimization algorithm (MLP-WOA). As a result of conceptual models, the IHACRES-based model better simulated the RR process in comparison to the GR4J, and MISD models. The effect of incorporating meteorological variables into the coupled hydrological process-based and machine learning models was also investigated where precipitation, wind speed, relative humidity, temperature and snow depth were added separately to each hydrological model. It is found that incorporating meteorological variables into the hydrological models increased the accuracy of the models in runoff simulation. Three different learning phases were successfully applied in the current study for improving runoff peak simulation accuracy. This study proved that phase one (only hydrological model) has a big error while phase three (coupling hydrological model by machine learning model) gave a minimum error in runoff estimation in a snow-covered catchment. The IHACRES-based MLP-WOA model with RMSE of 8.49 m3/s improved the performance of the ordinary IHACRES model by a factor of almost 27%. It can be considered as a satisfactory achievement in this study for runoff estimation through applying coupled conceptual-ML hydrological models. Recommended methodology in this study for RR modeling may motivate its application in alternative hydrological problems.
Neural network-based method for diagnosis and severity assessment of Graves’ orbitopathy using orbital computed tomography
Authors: Lee Jaesung , Seo Wangduk , Park Jaegyun , Lim Won-Seon , Oh Ja Young , Moon Nam Ju , Lee Jeong Kyu
Published: July 2022

Computed tomography (CT) has been widely used to diagnose Graves’ orbitopathy, and the utility is gradually increasing. To develop a neural network (NN)-based method for diagnosis and severity assessment of Graves’ orbitopathy (GO) using orbital CT, a specific type of NN optimized for diagnosing GO was developed and trained using 288 orbital CT scans obtained from patients with mild and moderate-to-severe GO and normal controls. The developed NN was compared with three conventional NNs [GoogleNet Inception v1 (GoogLeNet), 50-layer Deep Residual Learning (ResNet-50), and 16-layer Very Deep Convolutional Network from Visual Geometry group (VGG-16)]. The diagnostic performance was also compared with that of three oculoplastic specialists. The developed NN had an area under receiver operating curve (AUC) of 0.979 for diagnosing patients with moderate-to-severe GO. Receiver operating curve (ROC) analysis yielded AUCs of 0.827 for GoogLeNet, 0.611 for ResNet-50, 0.540 for VGG-16, and 0.975 for the oculoplastic specialists for diagnosing moderate-to-severe GO. For the diagnosis of mild GO, the developed NN yielded an AUC of 0.895, which is better than the performances of the other NNs and oculoplastic specialists. This study may contribute to NN-based interpretation of orbital CTs for diagnosing various orbital diseases