bluuebunny/crossref_metadata_2025 huggingface dataset:
Tensor dictionary learning for representing three-dimensional sound speed fields
Authors: Chen Panqi , Cheng Lei , Zhang Ting , Zhao Hangfang , Li Jianlong
Published: November 2022

Ocean sound speed field (SSF) representation is often plagued with low resolution (i.e., the capability of explaining fine-scale fluctuations). This drawback, however, is inherent in a number of classical SSF basis functions, e.g., empirical orthogonal functions, Fourier basis functions, and more recent tensor-based basis functions learned via the higher-order orthogonal iterative algorithm. For two-dimensional depth-time SSF representation, recent attempts relying on dictionary learning have shown that fine-scale sound speed information can be well preserved by a large number of basis functions. They are learned from the historical data without imposing rigid constraints on their shapes, e.g., the orthogonal constraints. However, generalizing the dictionary learning idea to represent three-dimensional (3D) spatial ocean SSF is non-trivial, in terms of both problem formulation and algorithm development. It calls for integrating the dictionary learning framework and the tensor-based basis function learning framework, a recently proposed one that captures the 3D sound speed correlations well. To achieve this goal, we develop a 3D SSF-tailored tensor dictionary learning algorithm that learns a large number of tensor-based basis functions with flexible shapes in a data-driven fashion. Numerical results based on the South China Sea 3D SSF data have showcased the superiority of the proposed approach over the prior method.
Protected areas provide thermal buffer against climate change
Authors: Xu Xiyan , Huang Anqi , Belle Elise , De Frenne Pieter , Jia Gensuo
Published: November 2022

Climate change is pushing temperatures beyond the thermal tolerance of many species. Whether protected areas (PAs) can serve as climate change refugia for biodiversity has not yet been explored. We find that PAs of natural (seminatural) vegetation effectively cool the land surface temperature, particularly the daily maximum temperature in the tropics, and reduce diurnal and seasonal temperature ranges in boreal and temperate regions, as compared to nonprotected areas that are often disturbed or converted to various land uses. Moreover, protected forests slow the rate of warming more at higher latitudes. The warming rate in protected boreal forests is up to 20% lower than in their surroundings, which is particularly important for species in the boreal where warming is more pronounced. The fact that nonprotected areas with the same type of vegetation as PAs show reduced warming buffer capacity highlights the importance of conservation to stabilize the local climate and safeguard biodiversity.
A versatile artificial metalloenzyme scaffold enabling direct bioelectrocatalysis in solution
Authors: Yang Xiaoti , Wu Wenjie , Chen Xiling , Wu Fei , Fan Shilong , Yu Ping , Mao Lanqun
Published: November 2022

Artificial metalloenzymes (ArMs) are commonly designed with protein scaffolds containing buried coordination pockets to achieve substrate specificity and product selectivity for homogeneous reactions. However, their reactivities toward heterogeneous transformations are limited because interfacial electron transfers are hampered by the backbone shells. Here, we introduce bacterial small laccase (SLAC) as a new protein scaffold for constructing ArMs to directly catalyze electrochemical transformations. We use molecular dynamics simulation, x-ray crystallography, spectroscopy, and computation to illustrate the scaffold-directed assembly of an oxo-bridged dicobalt motif on protein surface. The resulting ArM in aqueous phase catalyzes electrochemical water oxidation without mediators or electrode modifications. Mechanistic investigation reveals the role of SLAC scaffold in defining the four-electron transfer pathway from water to oxygen. Furthermore, we demonstrate that SLAC-based ArMs implemented with Ni
2+
, Mn
2+
, Ru
3+
, Pd
2+
, or Ir
3+
also enable direct bioelectrocatalysis of water electrolysis. Our study provides a versatile and generalizable route to complement heterogeneous repertoire of ArMs for expanded applications.
Ice-nucleating agents in sea spray aerosol identified and quantified with a holistic multimodal freezing model
Authors: Alpert Peter A. , Kilthau Wendy P. , O’Brien Rachel E. , Moffet Ryan C. , Gilles Mary K. , Wang Bingbing , Laskin Alexander , Aller Josephine Y. , Knopf Daniel A.
Published: November 2022

Sea spray aerosol (SSA) is a widely recognized important source of ice-nucleating particles (INPs) in the atmosphere. However, composition-specific identification, nucleation processes, and ice nucleation rates of SSA-INPs have not been well constrained. Microspectroscopic characterization of ambient and laboratory-generated SSA confirms that water-borne exudates from planktonic microorganisms composed of a mixture of proteinaceous and polysaccharidic compounds act as ice-nucleating agents (INAs). These data and data from previously published mesocosm and wave channel studies are subsequently used to further develop the stochastic freezing model (SFM) producing ice nucleation rate coefficients for SSA-INPs. The SFM simultaneously predicts immersion freezing and deposition and homogeneous ice nucleation by SSA particles under tropospheric conditions. Predicted INP concentrations agree with ambient and laboratory measurements. In addition, this holistic freezing model is independent of the source and exact composition of the SSA particles, making it well suited for implementation in cloud and climate models.
Controlling the uncontrollable: Quantum control of open-system dynamics
Authors: Kallush Shimshon , Dann Roie , Kosloff Ronnie
Published: November 2022

Control of open quantum systems is essential for the realization of contemporary quantum science and technology. We demonstrate such control using a thermodynamically consistent framework, taking into account the fact that the drive can modify the system’s interaction with the environment. Such an effect is incorporated within the dynamical equation, leading to control-dependent dissipation. This relation serves as the key element for open-system control. The control paradigm is displayed by analyzing entropy-changing state-to-state transformations, such as heating and cooling. The difficult task of controlling quantum gates is achieved for nonunitary reset maps with complete memory loss. In addition, we identify a mechanism for controlling unitary gates by actively removing entropy from the system to the environment. We demonstrate a universal set of single- and double-qubit unitary gates under dissipation.
Harnessing molecular isomerization in polymer gels for sequential logic encryption and anticounterfeiting
Authors: Dong Yu , Ling Yao , Wang Donghui , Liu Yang , Chen Xiaowei , Zheng Shiya , Wu Xiaosong , Shen Jinghui , Feng Shiyu , Zhang Jianyuan , Huang Weiguo
Published: November 2022

Using smart photochromic and luminescent tissues in camouflage/cloaking of natural creatures has inspired efforts to develop synthetic stimuli-responsive materials for data encryption and anticounterfeiting. Although many optical data-encryption materials have been reported, they generally require only one or a simple combination of few stimuli for decryptions and rarely offer output corruptibility that prevents trial-and-error attacks. Here, we report a series of multiresponsive donor-acceptor Stenhouse adducts (DASAs) with unprecedented switching behavior and controlled reversibility via diamine conformational locking and substrate free-volume engineering and their capability of sequential logic encryption (SLE). Being analogous to the digital circuits, the output of DASA gel–based data-encryption system depends not only on the present input stimulus but also on the sequence of past inputs. Incorrect inputs/sequences generate substantial fake information and lead attackers to the point of no return. This work offers new design concepts for advanced data-encryption materials that operate via SLE, paving the path toward advanced encryptions beyond digital circuit approaches.
Calibrating a thermometer for Earth’s interior over time
Authors: Asimow Paul D.
Published: November 2022

New high-pressure, high-temperature experiments refine our ability to trace the thermal evolution of the Earth’s interior using the geological record of intermittent, large-volume volcanic episodes.
Hormonal therapies up-regulate MANF and overcome female susceptibility to immune checkpoint inhibitor myocarditis
Authors: Zhang Yaohua , Sun Chengcao , Li Yajuan , Qin Juan , Amancherla Kaushik , Jing Ying , Hu Qingsong , Liang Ke , Zhang Zhao , Ye Youqiong , Huang Lisa A. , Nguyen Tina K. , Egranov Sergey D. , Zhao Zilong , Wu Andrew , Xi Yutao , Yao Jun , Hung Mien-Chie , Calin George A. , Cheng Jie , Lim Bora , Lehmann Lorenz H. , Salem Joe-Elie , Johnson Douglas B. , Curran Michael A. , Yu Dihua , Han Leng , Darabi Radbod , Yang Liuqing , Moslehi Javid J. , Lin Chunru
Published: November 2022

Immune checkpoint inhibitors (ICIs) have been increasingly used in combination for cancer treatment but are associated with myocarditis. Here, we report that tumor-bearing mice exhibited response to treatment with combinatorial anti–programmed cell death 1 and anti–cytotoxic T lymphocyte antigen–4 antibodies but also presented with cardiovascular toxicities observed clinically with ICI therapy, including myocarditis and arrhythmia. Female mice were preferentially affected with myocarditis compared to male mice, consistent with a previously described genetic model of ICI myocarditis and emerging clinical data. Mechanistically, myocardial tissue from ICI-treated mice, the genetic mouse model, and human heart tissue from affected patients with ICI myocarditis all exhibited down-regulation of
MANF
(mesencephalic astrocyte–derived neurotrophic factor) and
HSPA5
(heat shock 70-kDa protein 5) in the heart; this down-regulation was particularly notable in female mice. ICI myocarditis was amplified by heart-specific genetic deletion of mouse
Manf
and was attenuated by administration of recombinant MANF protein, suggesting a causal role. Ironically, both
MANF
and
HSPA5
were transcriptionally induced by liganded estrogen receptor β and inhibited by androgen receptor. However, ICI treatment reduced serum estradiol concentration to a greater extent in female compared to male mice. Treatment with an estrogen receptor β–specific agonist and androgen depletion therapy attenuated ICI-associated cardiac effects. Together, our data suggest that ICI treatment inhibits estradiol-dependent expression of
MANF/HSPA5
in the heart, curtailing the cardiomyocyte response to immune injury. This endocrine-cardiac-immune pathway offers new insights into the mechanisms of sex differences in cardiac disease and may offer treatment strategies for ICI myocarditis.
Selective decrease of donor-reactive T
regs
after liver transplantation limits T
reg
therapy for promoting allograft tolerance in humans
Authors: Tang Qizhi , Leung Joey , Peng Yani , Sanchez-Fueyo Alberto , Lozano Juan-Jose , Lam Alice , Lee Karim , Greenland John R. , Hellerstein Marc , Fitch Mark , Li Kelvin W. , Esensten Jonathan H. , Putnam Amy L. , Lares Angela , Nguyen Vinh , Liu Weihong , Bridges Nancy D. , Odim Jonah , Demetris Anthony J. , Levitsky Josh , Taner Timucin , Feng Sandy
Published: November 2022

Promoting immune tolerance to transplanted organs can minimize the amount of immunosuppressive drugs that patients need to take, reducing lifetime risks of mortality and morbidity. Regulatory T cells (T
regs
) are essential for immune tolerance, and preclinical studies have shown their therapeutic efficacy in inducing transplantation tolerance. Here, we report the results of a phase 1/2 trial (ARTEMIS, NCT02474199) of autologous donor alloantigen–reactive T
reg
(darT
reg
) therapy in individuals 2 to 6 years after receiving a living donor liver transplant. The primary efficacy endpoint was calcineurin inhibitor dose reduction by 75% with stable liver function tests for at least 12 weeks. Among 10 individuals who initiated immunosuppression withdrawal, 1 experienced rejection before planned darT
reg
infusion, 5 received darT
regs
, and 4 were not infused because of failure to manufacture the minimal infusible dose of 100 × 10
6
cells. darT
reg
infusion was not associated with adverse events. Two darT
reg
-infused participants reached the primary endpoint, but an insufficient number of recipients were treated for assessing the efficacy of darT
regs
. Mechanistic studies revealed generalized T
reg
activation, senescence, and selective reduction of donor reactivity after liver transplantation. Overall, the ARTEMIS trial features a design concept for evaluating the efficacy of T
reg
therapy in transplantation. The mechanistic insight gained from the study may help guide the design of future trials.
Dynamics of T cell repertoire renewal following autologous hematopoietic stem cell transplantation in multiple sclerosis
Authors: Ruder Josefine , Docampo María José , Rex Jordan , Obahor Simon , Naghavian Reza , Müller Antonia M.S. , Schanz Urs , Jelcic Ilijas , Martin Roland
Published: November 2022

Autologous hematopoietic stem cell transplantation (aHSCT) is a highly effective treatment of multiple sclerosis (MS). It depletes autoreactive cells and subsequently renews adaptive immune cells. The possible proinflammatory potential of surviving T cells early after aHSCT has not been studied. Here, we examined the dynamics of new and surviving T cells in 27 patients after aHSCT by multidimensional flow cytometry, T cell receptor (TCR) sequencing, specificity testing, telomere length profiling, and HLA genotyping. Early after aHSCT, naïve T cells are barely detectable, whereas effector memory (EM) T cells quickly reconstitute to pre-aHSCT values. EM CD4
+
T cells early after aHSCT have shorter telomeres, have higher expression of senescence and exhaustion markers, and proliferate less than those before aHSCT. We find a median TCR repertoire overlap of 26% between the early post-aHSCT EM CD4
+
T cells and pre-aHSCT, indicating persistence of EM CD4
+
T cells early after transplantation. The EM CD4
+
TCR repertoire overlap declines to 15% at 12 months after aHSCT, whereas the naïve TCR repertoire entirely renews. HLA-DR–associated EM CD4
+
T cell reactivity toward MS-related antigens decreased after aHSCT, whereas reactivity toward EBV increased. Our data show substantial survival of pre-aHSCT EM CD4
+
T cells early after transplantation but complete renewal of the T cell repertoire by nascent T cells later.
MIR155HG Plays a Bivalent Role in Regulating Innate Antiviral Immunity by Encoding Long Noncoding RNA-155 and microRNA-155-5p
Authors: Rai Kul Raj , Liao Yuan , Cai Mengjuan , Qiu Haori , Wen Faxin , Peng Min , Wang Song , Liu Shasha , Guo Guijie , Chi Xiaojuan , Maarouf Mohamed , Chen Yuhai , Huang Shile , Chen Ji-Long
Published: November 2022

Here, we found that lncRNA-155KO mice lacking most of the lncRNA-155 sequences along with pre-miRNA-155, were more susceptible to influenza virus or pseudorabies virus infection than miRNA-155KO mice lacking only 19 bp of the miRNA-155 core sequence without affecting the expression of lncRNA-155, as evidenced by faster body weight loss, poorer survival, and higher viral load, suggesting an additional role of lncRNA-155 in regulating viral pathogenesis besides via processing miRNA-155. Congruously, miRNA-155-deleted lncRNA-155 significantly attenuated the viral infection.
Complete Genome Sequence of Gordonia rubripertincta Bacteriophage Hexbug Suggests Potential for a New CT Subcluster
Authors: Barszczak Daniel J. , Allison Maxwell J. , Cai Yaqi , Forman Lily , Goldstein Joshua M. , Hakimjee Sarrah M. , Scapicchio Matthew T. , Torres Ruben , Gavin Hannah E.
Published: November 2022

Through the SEA-PHAGES program at Tufts University, a bacteriophage infecting
Gordonia rubripertincta
NRRL B-16540 was isolated and characterized. Hexbug is a lytic phage and is currently one of 44 phages belonging to cluster CT. The Hexbug genome shares >96% nucleotide identity with cluster CT phage Orla.
Metagenome-Assembled Genome of a Putative Methanogenic
Methanosarcina
sp. Strain Enriched from Terrestrial High-CO
2
Subsurface Sediments
Authors: Jia Zeyu , Lipus Daniel , Bartholomäus Alexander , Burckhardt Oliver , Sondermann Megan , Wagner Dirk , Kallmeyer Jens
Published: November 2022

A metagenome-assembled genome (MAG), named
Methanosarcina
sp. strain ERenArc_MAG2, was obtained from a 3-month-old H
2
/CO
2
atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere.
Mucosal and Systemic Responses to Severe Acute Respiratory Syndrome Coronavirus 2 Vaccination Determined by Severity of Primary Infection
Authors: Sajadi Mohammad M. , Myers Amber , Logue James , Saadat Saman , Shokatpour Narjes , Quinn James , Newman Michelle , Deming Meagan , Rikhtegaran Tehrani Zahra , Magder Laurence S. , Karimi Maryam , Abbasi Abdolrahim , Shlyak Mike , Baracco Lauren , Frieman Matthew B. , Crotty Shane , Harris Anthony D.
Published: November 2022

This study on SARS2 vaccination in those with and without previous exposure to the virus demonstrates that severity of infection dictates IgA responses in primary infection as well as response to vaccination (peak responses and durability), which could have implications for continued protection against reinfection.
Probiotic Bifidobacteria Mitigate the Deleterious Effects of
para
-Cresol in a Drosophila melanogaster Toxicity Model
Authors: Stuivenberg Gerrit A. , Chmiel John A. , Akouris Polycronis P. , Burton Jeremy P. , Reid Gregor
Published: November 2022

Chronic kidney disease (CKD) affects approximately 10% of the global population and has limited treatment options. The accumulation of gut microbiota-derived uremic toxins, such as
para
-cresol (
p
-cresol) and
p-
cresyl sulfate, is associated with the onset of comorbidities (i.e., atherosclerosis and cognitive disorders) in CKD.
Methanogen Levels Are Significantly Associated with Fecal Microbiota Composition and Alpha Diversity in Healthy Adults and Irritable Bowel Syndrome Patients
Authors: Wang Taojun , van Dijk Leander , Rijnaarts Iris , Hermes Gerben D. A. , de Roos Nicole M. , Witteman Ben J. M. , de Wit Nicole J. W. , Govers Coen , Smidt Hauke , Zoetendal Erwin G.
Published: November 2022

Hydrogenotrophic microbes play an essential role in the disposal of hydrogen and the maintenance of the hydrogen balance in gut ecosystems. Their abundances vary between individuals and have been reported to be associated with human gut disorders such as irritable bowel disease.
A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota
Authors: Zhang Xiao-Xuan , Lv Qing-Bo , Yan Qiu-Long , Zhang Yue , Guo Ruo-Chun , Meng Jin-Xin , Ma He , Qin Si-Yuan , Zhu Qing-He , Li Chun-Qiu , Liu Rui , Liu Gang , Li Sheng-Hui , Sun Dong-Bo , Ni Hong-Bo
Published: November 2022

We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species.
Ejaculate for Microbiological Culture: To Wash or Not To Wash?
Authors: Theiler Tom , Olaru Ioana Diana , Kilzer Charlotte , Schuler Franziska , Schaumburg Frieder
Published: November 2022

This study compares two methods for processing ejaculate samples from men undergoing investigations for infertility. The method of sample washing and centrifugation was compared to the standard method of direct inoculation and culture.
Heavy Mo isotope composition of northern Bataan adakites, Philippines: Evidence for fore-arc subduction erosion?
Authors: Liu Hai-Quan , Li Jie , Xu Yi-Gang , Yumul Graciano P. , Knittel Ulrich , Dimalanta Carla B. , Payot Betchaida D. , Queaño Karlo , Huang Xiao-Long , Zhang Le
Published: November 2022

The identification of an eroded fore-arc crust component in arc magmas is challenging due to the combined effects of mantle metasomatism and crustal assimilation–fractional crystallization. In this study, molybdenum (Mo) isotope compositions are used in conjunction with Sr-Nd-Hf isotopic and elemental data to identify eroded fore-arc crust components in adakites from the Cuyapo and Balungao volcanoes of the northern Bataan segment of the Luzon arc (Philippines). The Mo isotopic ratios (δ98/95Mo, relative to the NIST SRM 3134 standard) of these adakites increase with increasing εNd (+4.3 to +5.6) and Ba/Nb (206–286). The low δ98/95Mo (−0.36‰ to −0.26‰) in the Cuyapo adakites coupled with low Sr-Nd-Hf isotopic ratios suggests contributions from the residual slab, which lost isotopically heavy Mo during dehydration. Interestingly, the high δ98/95Mo (−0.18‰ to 0.00‰) Balungao adakites have Mo-Sr-Nd-Hf isotopic ratios similar to those of the Luzon basement. Fractionated Nb/Ta (16–18) and high Sr/Y indicate the coexistence of melt with residual rutile and garnet ± amphibole assemblages, corresponding to a source region (>~45 km) below the present Luzon crust (~33 km). This thus suggests an origin of heavy Mo from partial melting of eroded crust in the mantle wedge rather than in the upper-plate crust. Our work not only demonstrates that Mo isotopes may be a potential tracer of eroded crust but also highlights that lavas with combined high δ98/95Mo, εNd, and Ba/Nb emplaced at subduction zones with juvenile arc crust may be a result of subduction erosion.
Pellagra as a differential diagnosis in the confused patient on the acute medical unit
Authors: Tew Jennifer Catherine , Harrington Laura , Elsayed Haythum , Mlawa Gideon
Published: November 2022

A man in his 80s was admitted via the acute medical take after presenting with increased confusion and features of alcohol withdrawal. He had a several-month history of a worsening pruritic rash surrounding his neck, arms and legs in addition to new, profuse diarrhoea. In view of the background of known chronic alcoholism and the coexisting symptoms of rash, confusion and diarrhoea, pellagra was diagnosed via a multidisciplinary approach. Oral nicotinamide supplementation was commenced and his symptoms responded rapidly. The bias and challenge of reaching a unified diagnosis in the context of a multisystem condition are exemplified in this case report.
Characterising collateral vessels in eyes with branch retinal vein occlusions using widefield swept-source optical coherence tomography angiography
Authors: Rudnick Noam D , Vingopoulos Filippos , Wang Jay C , Garg Itika , Cui Ying , Zhu Ying , Le Rongrong , Katz Raviv , Lu Yifan , Patel Nimesh A , Miller John B
Published: November 2022

Background/aims

To characterise the morphology, location and functional significance of both macular and extramacular collateral vessels (CVs) in patients with a history of branch retinal vein occlusion (BRVO) using widefield swept-source optical coherence tomography angiography (WF SS OCTA).

Methods

Patients with a history of BRVO underwent WF SS OCTA testing to acquire 12×12 mm images, which were evaluated for CVs and non-perfusion area (NPA). Region of interest analysis of individual CVs was performed to identify correlations between CV size, depth and retinal location. Mixed effects multivariate regression analyses of factors associated with NPA and visual acuity (VA) were performed.

Results

Fifty-five CVs were identified in 28 BRVO eyes from 27 patients. CVs were identified in 42.9% (12/28) of eyes with a history of BRVO, and of these, 45.5% (25/55) were extramacular. The majority of CVs (87.3%, 48/55) coursed through both the superficial and the deep capillary plexus (DCP), while a subset (12.7%, 7/55) were strictly superficial. No CVs were found to course strictly through the DCP alone. CV depth increased with distance from the optic disc (p=0.011) and CV size increased with distance from the fovea (p=0.005). There were no statistically significant associations between CVs and NPA, or between CVs and VA.

Conclusions

WF SS OCTA revealed that a large fraction of CVs that form after BRVO are extramacular, and the morphology of CVs varies as a function of retinal location. Depth-resolved study of CVs may offer valuable insights on the pathophysiological mechanisms leading to the development of macular oedema.
Exploring the role of intratendinous pressure in the pathogenesis of tendon pathology: a narrative review and conceptual framework
Authors: Pringels Lauren , Cook Jill L , Witvrouw Erik , Burssens Arne , Vanden Bossche Luc , Wezenbeek Evi
Published: November 2022

Despite the high prevalence of tendon pathology in athletes, the underlying pathogenesis is still poorly understood. Various aetiological theories have been presented and rejected in the past, but the tendon cell response model still holds true. This model describes how the tendon cell is the key regulator of the extracellular matrix and how pathology is induced by a failed adaptation to a disturbance of tissue homeostasis. Such failure has been attributed to various kinds of stressors (eg, mechanical, thermal and ischaemic), but crucial elements seem to be missing to fully understand the pathogenesis. Importantly, a disturbance of tissue pressure homeostasis has not yet been considered a possible factor, despite it being associated with numerous pathologies. Therefore, we conducted an extensive narrative literature review on the possible role of intratendinous pressure in the pathogenesis of tendon pathology. This review explores the current understanding of pressure dynamics and the role of tissue pressure in the pathogenesis of other disorders with structural similarities to tendons. By bridging these insights with known structural changes that occur in tendon pathology, a conceptual model was constituted. This model provides an overview of the possible mechanism of how an increase in intratendinous pressure might be involved in the development and progression of tendon pathology and contribute to tendon pain. In addition, some therapies that could reduce intratendinous pressure and accelerate tendon healing are proposed. Further experimental research is encouraged to investigate our hypotheses and to initiate debate on the relevance of intratendinous pressure in tendon pathology.
Cross-sectional observational study protocol: missing microbes in infants born by caesarean section (MiMIC): antenatal antibiotics and mode of delivery
Authors: Warda Alicja K , Dempsey Eugene M , Forssten Sofia D , Ryan C Anthony , Cryan John F , Patterson Elaine , O'Riordan Mairead N , O’Shea Carol-Anne , Keohane Finola , Meehan Grainne , O’Connor Orlagh , Ross R Paul , Stanton Catherine
Published: November 2022

Introduction

The intestinal microbiome in early life plays a major role in infant health and development. Factors like antibiotic exposure, breast/formula feeding and mode of delivery are known to affect the microbiome. The increasing occurrence of caesarean section (C-section) deliveries and antibiotic exposure warrants further insight into the potential missing microbes in those infants. The study objective is to study the effect of maternal antibiotic administration during pregnancy and/or C-section mode of delivery on the development of the infant’s intestinal microbiome until the age of 2 years.

Methods and analysis

A single site, cross-sectional observational study of C-section and vaginally delivered infants being either exposed to maternal antibiotic treatment or not during the third trimester of pregnancy. Throughout the nine visits, stool, urine, saliva, hair, breast milk and vaginal swabs will be collected from either mother and/or infant for microbiome and metabolomic analysis.

Ethics and dissemination

The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. The trial has been registered at ClinicalTrials.gov.

The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases.

Trial registration number

NCT04134819.
Emergency department visits and emergency-to-inpatient admissions for abnormal uterine bleeding in the USA nationwide
Authors: Grubman Jessica , Hawkins Mitzi , Whetstone Sara , Autry Meg , Lazar Ann , Sawaya George F , Jacoby Vanessa
Published: November 2022

Background

Abnormal uterine bleeding (AUB) is a common but understudied gynaecological problem, and data are lacking on emergency department (ED) visits and associated ED-to-inpatient admissions for AUB. This project aims to further understanding of the burden of AUB on patients and the healthcare system by establishing the number and characteristics of women with AUB in the ED and evaluating predictors of AUB-related inpatient hospitalisation in the USA.

Methods

This is a cross-sectional study of women presenting to the ED with non-malignant AUB in the 2016 US Nationwide Emergency Department Sample (NEDS). Clinical, demographic and hospital system factors were evaluated. χ2and Mann-Whitney tests were used to compare the proportion of visits with each characteristic, resulting in inpatient admission versus discharge from the ED. Multivariable logistic regression models were used to analyse predictors of AUB in the ED and of AUB-related hospitalisations.

Results

There were 1.03 million AUB-related visits in the 2016 NEDS, of which 11.2% resulted in inpatient admission. Clinical as well as demographic and hospital system factors influenced ED disposition. Women with AUB tended to be of reproductive age, be underinsured, live in lower income and urban areas, and present to urban and public hospitals. However, older age, higher income, better insurance, presentation to private hospitals and rural residence predicted inpatient admission.

Conclusions

Our study highlights the ED as an essential place of care for women with AUB while also demonstrating the importance of access to outpatient gynaecology services as some AUB-related ED visits may be preventable with outpatient care. The significant demographic and hospital system differences, as well as expected clinical differences, between women with AUB admitted to inpatient and women discharged from the ED imply structural biases impacting AUB-related ED care and add to the deepening understanding of health disparities.
KITgenetic alterations in breast cancer
Authors: Vahdatinia Mahsa , Derakhshan Fatemeh , Da Cruz Paula Arnaud , Dopeso Higinio , Marra Antonio , Gazzo Andrea M , Brown David , Selenica Pier , Ross Dara S , Razavi Pedram , Zhang Hong , Weigelt Britta , Wen Hannah Y , Brogi Edi , Reis-Filho Jorge S , Pareja Fresia
Published: November 2022

Aims

Activating somatic mutations or gene amplification ofKITresult in constitutive activation of its receptor tyrosine kinase, which is targetable in various solid tumours. Here, we sought to investigate the presence ofKITgenetic alterations in breast cancer (BC) and characterise the histological and genomic features of these tumours.

Methods

A retrospective analysis of 5,575 BCs previously subjected to targeted sequencing using the FDA-authorised Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay was performed to identify BCs withKITalterations. A histological assessment ofKIT-altered BCs was conducted, and their repertoire of genetic alterations was compared with that of BCs lackingKITgenetic alterations, matched for age, histological type, oestrogen receptor/HER2 status and sample type.

Results

We identified 18 BCs (0.32%), including 9 primary and 9 metastatic BCs, with oncogenic/likely oncogenic genetic alterations affectingKIT, including activating somatic mutations (n=4) or gene amplification (n=14). AllKIT-altered BCs were of high histological grade, although no distinctive histological features were observed. When compared with BCs lackingKITgenetic alterations, no distinctive genetic features were identified. In two metastaticKIT-altered BCs in which the matched primary BC had also been analysed by MSK-IMPACT, theKITmutations were found to be restricted to the metastatic samples, suggesting that they were late events in the evolution of these cancers.

Conclusions

KITgenetic alterations are vanishingly rare in BC.KIT-altered BCs are of high grade but lack distinctive histological features. Genetic alterations inKITmight be late events in the evolution and/or progression of BC.
Trusted research environments are definitely about trust
Authors: Affleck Paul , Westaway Jenny , Smith Maurice , Schrecker Geoff
Published: November 2022

In their highly topical paper, Grahamet alargued that Trusted Research Environments (TREs) are not actually about trust because they reduce or remove ‘…the need for trust in the use and sharing of patient health data’. We believe this is fundamentally mistaken. TREs mitigate or remove some risks, but they do not address all public concerns. In this regard, TREs provide evidence for people to decide whether the bodies holding and using their data can be trusted. TREs may make it easier for people to trust but there is still a need for that trust.
Association of obesity with disease outcome in multiple sclerosis
Authors: Lutfullin Isabel , Eveslage Maria , Bittner Stefan , Antony Gisela , Flaskamp Martina , Luessi Felix , Salmen Anke , Gisevius Barbara , Klotz Luisa , Korsukewitz Catharina , Berthele Achim , Groppa Sergiu , Then Bergh Florian , Wildemann Brigitte , Bayas Antonios , Tumani Hayrettin , Meuth Sven G , Trebst Corinna , Zettl Uwe K , Paul Friedemann , Heesen Christoph , Kuempfel Tania , Gold Ralf , Hemmer Bernhard , Zipp Frauke , Wiendl Heinz , Lünemann Jan D
Published: November 2022

Background

Obesity reportedly increases the risk for developing multiple sclerosis (MS), but little is known about its association with disability accumulation.

Methods

This nationwide longitudinal cohort study included 1066 individuals with newly diagnosed MS from the German National MS cohort. Expanded Disability Status Scale (EDSS) scores, relapse rates, MRI findings and choice of immunotherapy were compared at baseline and at years 2, 4 and 6 between obese (body mass index, BMI ≥30 kg/m2) and non-obese (BMI <30 kg/m2) patients and correlated with individual BMI values.

Results

Presence of obesity at disease onset was associated with higher disability at baseline and at 2, 4 and 6 years of follow-up (p<0.001). Median time to reach EDSS 3 was 0.99 years for patients with BMI ≥30 kg/m2 and 1.46 years for non-obese patients. Risk to reach EDSS 3 over 6 years was significantly increased in patients with BMI ≥30 kg/m2compared with patients with BMI <30 kg/m2after adjustment for sex, age, smoking (HR 1.87; 95% CI 1.3 to 2.6; log-rank test p<0.001) and independent of disease-modifying therapies. Obesity was not significantly associated with higher relapse rates, increased number of contrast-enhancing MRI lesions or higher MRI T2 lesion burden over 6 years of follow-up.

Conclusions

Obesity in newly diagnosed patients with MS is associated with higher disease severity and poorer outcome. Obesity management could improve clinical outcome of MS.
Biomarkers to predict risk of venous thromboembolism in patients with rheumatoid arthritis receiving tofacitinib or tumour necrosis factor inhibitors
Authors: Weitz Jeffrey I , Szekanecz Zoltán , Charles-Schoeman Christina , Vranic Ivana , Sahin Burak , Paciga Sara A , Wang Zhenyu , Hyde Craig , Martin David A
Published: November 2022

Objective

In the ORAL (Oral Rheumatoid Arthritis triaL) Surveillance study of patients with rheumatoid arthritis aged ≥50 years with ≥1 additional cardiovascular risk factor, incidence of pulmonary embolism was higher with tofacitinib 10 mg two times per day than with tumour necrosis factor inhibitors (TNFi). This exploratory post hoc analysis examined whether biomarkers explained the associations of tofacitinib versus TNFi with venous thromboembolism (VTE).

Methods

ORAL Surveillance was a prospective, open-label, event-driven, non-inferiority, postauthorisation safety study. Patients were randomised 1:1:1 to receive tofacitinib 5 mg or 10 mg two times per day or a TNFi. For this analysis, 294 soluble, proteomic, genetic and antibody biomarkers (of which 79 had a known role in inflammation, coagulation, vascular biology or Janus kinase signalling) were quantified in serum collected at baseline, month 12 and study end.

Results

Overall, 4362 patients were randomised and treated. The exploratory biomarker data set included 285 patients (57 VTE cases; 228 matched controls). D-dimer was quantified in 3732 patients (54 VTE cases; 3678 controls). No biomarker demonstrated a clear mechanistic association with the increased risk of VTE for tofacitinib versus TNFi. Month 12 D-dimer levels were positively associated with risk of a subsequent VTE within the tofacitinib 5 mg and 10 mg two times per day arms.

Conclusions

Overall, this post hoc analysis did not identify biomarkers that explained the increased VTE risk for tofacitinib versus TNFi. Individual VTE risk should be considered when making decisions about initiation or maintenance of tofacitinib treatment.

Trial registration number

NCT02092467; ClinicalTrials.gov.
The influence of forest harvesting activities on seismic line tree and shrub regeneration in upland mixedwood boreal forests
Authors: Van Dongen Angeline , Jones Caren , Schoonmaker Amanda , Harvey Jill , Degenhardt Dani
Published: November 2022

Alberta's forests are becoming increasingly disturbed and fragmented by the cumulative effects of anthropogenic disturbances exacerbated by the enduring footprint of seismic lines on the landscape. Forest harvesting and subsequent reforestation activities (e.g., site preparation and tree planting) may facilitate tree growth on seismic lines when forestry companies incorporate them into management areas. In this study, forest regeneration was assessed along transects on and off seismic lines within four cutblocks in northwestern Alberta. Tree, sapling, and shrub characteristics were measured, and tree cookies from a subset of trees on and off seismic lines were used to model height growth. No difference in total tree, sapling, or shrub counts on and off seismic lines was found although trees on seismic lines were growing at slightly slower rates compared to the adjacent cutblock, and Alnus viridis was more abundant on seismic lines. Our results suggest that, despite some species-level differences and modest differences in tree growth rates, trees on seismic lines within cutblocks are regenerating similarly to other trees growing in the post-harvest stand. These findings indicate that forest harvesting, and subsequent reforestation, could represent an important tool in conducting landscape-level restoration in mixedwood forests where seismic lines have not naturally recovered.
Simulation and Experiment Study on Energy Absorption of a Thin-Walled Tube Component with Vertical Strip
Authors: Wang Cheng Long , Shang Huan , Liu Guo Ming , Zhang Ji Wei , Chen Yi Fang
Published: November 2022

In order to better solve anti-impact problem of hydraulic support, based on the previous study of anti-impact device by the author’s team, a thin-walled tube component with vertical strip which works as an energy absorbing component is designed and simulation model of the component is established, and energy absorption characteristics of the component is studied. Experimental verification is done and the simulation model is optimized based on the experimental data. Based on the above works, parameters of the component are re-optimized and energy absorption characteristics of the component are tested. Through supporting reaction force–deformation curve of the thin-walled tube component with vertical strip, it can be seen that deformation stability of the component is high, and the initial peak force difference ratio of energy absorbing components before and after structural optimization is reduced from 4.8% to 1.04%. The results show that energy absorption characteristics of the thin-walled tube component with vertical strip are further improved, and accuracy of the simulation model is also further improved.
Sensitivity Analysis and Robust Assignment of Natural Frequencies for Vibrating Systems Using the Receptance Method
Authors: Zhang Lin , Zhang Tao , Ouyang Huajiang , Li Tianyun , Xu Genghui
Published: November 2022

This paper presents a new receptance-based method for the robust assignment of natural frequencies. This method aims to address the deviation of the actually achieved natural frequencies for target natural frequencies when assigning natural frequencies, which usually arises due to uncertainties in passive structural modifications (i.e. mass and stiffness modifications). The mathematical expression is derived for the sensitivity of the target natural frequency to the uncertainties in modification parameters, which are subsequently employed to characterize the potential deviations of the target natural frequencies in the total differential form. The obtained deviation expression is integrated into the optimization calculation of the natural frequency assignment as an extra penalty term to boost the acquisition of highly robust modification parameters. The proposed robust assignment method, as a non-probabilistic technique, can be employed without any knowledge of the probabilistic distribution of uncertainty in modification parameters. Moreover, it uses only the measured frequency response functions (FRFs), preserving the advantage of the receptance method not needing a numerical model. Two numerical examples and a comparison with a typical eigenstructure assignment method (reported in the literature) demonstrate that the proposed method can provide highly robust modification parameter solutions. The application of the proposed method to the natural frequency assignment of a laboratory water-filled pipeline system gives experimental evidence of its effectiveness.
Study on Evaluation of Development of Guilin E-Government Based on E-Government Development Index
Authors: Xiao Libin
Published: November 2022

E-government has become an important direction for the development of our government. Measuring national and regional e-government development indicators can help government agencies better understand the actual situation of e-government. This paper is based on E-government Development Index, including the Online Services Index (OSI), Telecommunications Infrastructure Index (TII) and Human Capital Index (HCI). The development of e-government in Guilin is evaluated by using the methods of index change analysis and comparative analysis. The relevant data of this paper come from Guangxi Statistical Yearbook, Guilin Economic and Social Statistical Yearbook and the official website of Guilin Bureau of Statistics. From the study of Guilin e-government data, we judged that Guilin e-government is in the trend of rapid development and comprehensive and coordinated development. Through its development trend, we can judge that in the future, Guilin e-government will continue to develop, but at the same time, if we do not deal with the relationship between development speed and development content, it will also bring great trouble to Guilin e-government. Therefore, we put forward the following development suggestions: (1) Guilin e-government should strengthen technological innovation and development, and create an intelligent e-government platform. (2) Guilin e-government will make government services more targeted and build a service platform for special groups. (3) Guilin e-government should formulate e-government policies and improve institutional innovation.
Reinforcement Learning for Bipedal Gait with MAX-E2 Humanoid Robot
Authors: Yanguas-Rojas David , Mojica-Nava Eduardo , Cardenas Alben
Published: November 2022

We consider the whole-body humanoid gait control model via reinforcement learning, where an initial predefined parametric gait policy is optimized by employing the augmented random search algorithm realizing most of the experiments in simulation and verifying the results onto the real robot. In our proposal, we take into account the reality gap problem, also known as Sim to real problem, for the development of the experiments and the policy guaranteeing functional results in the real robot employing a simplified custom simulator. We show that our proposed learning algorithm allows the humanoid robot MAX-E2 to walk efficiently in virtual and real environments.
Geodesic conjugacy for geodesically reversible Finsler metrics
Authors: Kim Chang-Wan
Published: November 2022

A Finsler metric is geodesically reversible if geodesic remain geodesics after a change of orientation. For a reversible Minkowski space, we alter the geodesically reversible Finsler metric without conjugate points in a strictly convex compact subset and show that its central symmetrization is geodesically conjugate to the original reversible Minkowski norm.
Coefficient inequalities for a subfamily of Sakaguchi functions
Authors: Rai Pratima , Kumar Sushil
Published: November 2022

In this paper, we explore a subfamily of starlike functions with respect to symmetric points allied with the hyperbolic cosine function. We study Hermitian–Toeplitz determinants of third and fourth orders for the functions belonging to this subfamily. Further, we calculate estimates on the initial successive inverse coefficients as well as logarithmic coefficients and related functionals for such functions. In addition, we also determine bounds on Hankel determinants of third order and symmetric Toeplitz determinants of second and third orders.
On homological classification of monoids by Condition (E′P) of right S-acts
Authors: Nouri Leila , Saany Hossein Mohammadzadeh , Khamechi Pouyan
Published: November 2022

In 2006, Condition [Formula: see text] was introduced by Golchin and Mohammadzadeh and the theorems associated with it were proved. In this paper, we continue the study in relation to the above condition and for some of the properties in the [Formula: see text]-acts. We present the equivalent on the basis of that, which in turn illustrates the importance of this condition. Given that Condition [Formula: see text] is the generalization of Conditions [Formula: see text] and [Formula: see text], so the study of the condition in relation to other properties of the [Formula: see text]-acts will give a better understanding of the behavior of the [Formula: see text]-acts and even Conditions [Formula: see text] and [Formula: see text].
Applications of the q-Wanas operator for a certain family of bi-univalent functions defined by subordination
Authors: Wanas Abbas Kareem , Mahdi Ahmed Mohsin
Published: November 2022

In this work, we introduce and investigate a certain family [Formula: see text] of holomorphic and bi-univalent functions which are defined in the open unit disk [Formula: see text] associated with [Formula: see text]-Wanas operator. The estimates on the initial Taylor–Maclaurin coefficients [Formula: see text] and [Formula: see text] for the certain family are obtained. Also, we solve the Fekete–Szegö type inequality for functions in this family.