bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between bacteria and outcome and the influence of sampling method, in people with a diabetic foot infection
Authors: Gramberg Meryl Cinzía Tila Tamara , Mahadew Shaya Krishnaa Normadevi , Lissenberg-Witte Birgit Ilja , Bleijenberg Marielle Petra , de la Court Jara Rebekka , van Hattem Jarne Marijn , Sabelis Louise Willy Elizabeth , Lagrand Rimke Sabine , de Groot Vincent , Heijer Martin Den , Peters Edgar Josephus Gerardus 
Published: July 2022

Abstract
Purpose
Different bacteria lead to divers diabetic foot infections (DFIs), and some bacteria probably lead to higher amputation and mortality risks. We assessed mortality and amputation risk in relation to bacterial profiles in people DFI and investigated the role of sampling method.

Methods
We included people (> 18 years) with DFI in this retrospective study (2011–2020) at a Dutch tertiary care hospital. We retrieved cultures according to best sampling method: (1) bone biopsy; (2) ulcer bed biopsy; and (3) swab. We aggregated data into a composite determinant, consisting of unrepeated bacteria of one episode of infection, clustered into 5 profiles: (1) Streptococcus and Staphylococcus aureus; (2) coagulase-negative Staphylococcus, Cutibacterium, Corynebacterium and Enterococcus; (3) gram-negative; (4) Anaerobic; and (5) less common gram-positive bacteria. We calculated Hazard Ratio’s (HR’s) using time-dependent-Cox regression for the analyses and investigated effect modification by sampling method.

Results
We included 139 people, with 447 person-years follow-up and 459 episodes of infection. Sampling method modified the association between bacterial profiles and amputation for profile 2. HR’s (95% CI’s) for amputation for bacterial profiles 1–5: 0.7 (0.39–1.1); stratified analysis for profile 2: bone biopsy 0.84 (0.26–2.7), ulcer bed biopsy 0.89 (0.34–2.3), swab 5.9*(2.9–11.8); 1.3 (0.78–2.1); 1.6 (0.91–2.6); 1.6 (0.58–4.5). HR’s (95% CI’s) for mortality for bacterial profiles 1–5: 0.89 (0.49–1.6); 0.73 (0.38–1.4); 2.6*(1.4–4.8); 1.1(0.58–2.2); 0.80(0.19–3.3).

Conclusions
In people with DFI, there was no association between bacterial profiles in ulcer bed and bone biopsies and amputation. Only in swab cultures, low-pathogenic bacteria (profile 2), were associated with a higher amputation risk. Infection with gram-negative bacteria was associated with a higher mortality risk. This study underlined the possible negative outcome of DFI treatment based on swabs cultures.
Aspect term extraction via information-augmented neural network
Authors: Liu Ning , Shen Bo 
Published: July 2022

AbstractAspect term extraction (ATE) aims at identifying the aspect terms that are expressed in a sentence. Recently, Seq2Seq learning has been employed in ATE and significantly improved performance. However, it suffers from some weaknesses, such as lacking the ability to encode the more informative information and integrate information of surrounding words in the encoder. The static word embeddings employed in ATE fall short of modeling the dynamic meaning of words. To alleviate the problems mentioned above, this paper proposes the information-augmented neural network (IANN) which is a novel Seq2Seq learning framework. In IANN, a specialized neural network is developed as the key module of the encoder, named multiple convolution with recurrence network (MCRN), to encode the more informative information and integrate information of surrounding words in the encoder. The contextualized embedding layer is designed to capture the dynamic word sense. Besides, the novel AO ({Aspect, Outside}) tags are proposed as the less challenging tagging scheme. A lot of experiments have been performed on three widely used datasets. These experiments demonstrate that the proposed IANN acquires state-of-the-art results and validate that the proposed IANN is a powerful method for the ATE task.
Biochar aerogel-based electrocatalyst towards efficient oxygen evolution in acidic media
Authors: Hui Bin , Chen Hongjiao , Zhou Chengfeng , Cai Liping , Zhang Kewei , Quan Fengyu , Yang Dongjiang 
Published: July 2022

AbstractThe controllable synthesis of oxygen evolution reaction (OER) electrocatalyst is an urgent need to advance the development of sustainable energy conversion and storage. However, the OER efficiency in acidic media is seriously hindered by slow reaction kinetics. The traditional acidic OER electrocatalysts are more prone to be oxidized and corroded as results of unstable carrier structures and variable electronic states of active species. Herein, a high-performing biochar aerogel (BA) based electrocatalyst were realistically designed and synthetized via joint utilization of the terrestrial lignin and seaweed polysaccharide as carbon sources. Originating from the induction effect of "egg-box" structure in alginate and the self-template effect of lignosulfonate, the BA decorated with Ru/RuS2 particles was synthesized triumphantly. The as-synthesized electrocatalyst required a low overpotential of 228 mV to attain 10 mA cm−2 in 0.5 M H2SO4 and exhibited a good stability for over 12,000 s. The good activity was strongly dependent on the assembled unique two-dimensional/three-dimensional (2D/3D) channels in carbon aerogels. Notably, the numerous defective sites at carbon could strongly interact with the Ru/RuS2 heterojunction for remarkably enhancing the catalytic activity and stability of whole catalytic system in acidic media. This work puts forward a novel and effective strategy towards the enhancement of the acidic OER process by rational regulations of the BA and the coupling effect in micro-interface.
Graphical Abstract
Araucariaceous fossil woods from the Upper Triassic Ischigualasto Formation (San Juan Province, Argentina): paleofloristic and paleoclimatic implications
Authors: Bodnar Josefina , Sagasti Ana Julia , Correa Gustavo A. , Miranda Victoria , Medina Florencia 
Published: July 2022

AbstractIn this contribution, fossil woods from the Valle de La Luna Member of the Upper Triassic Ischigualasto Formation at Ischigualasto Provincial Park, San Juan Province, Argentina, are described. The specimens are preserved as silica permineralization in tuffs intercalated with carbonaceous mudstone beds interpreted as distal floodplain facies. The fossil woods were assigned to the new species Agathoxylon argentinum since their anatomy differs from the known Mesozoic Gondwanan species of the genus Agathoxylon. The combination of characters present in the new taxon indicates an affiliation with the conifer family Araucariaceae. Signals of fungal-mediated wood decay were observed, comparable to the activity of basidiomycetes. Spherical structures attached to the walls of the tracheids were recognized and are interpreted as holocarpic chytrid fungi. The growth rings were quantitatively analyzed. Low values of percentage diminution, percentage latewood, and Ring Markedness Index, and a mean percentage skew of +11.5, were obtained, suggesting that the new species was an evergreen gymnosperm. The stratigraphic distribution and taxonomic composition of the Ischigualasto Formation fossil-plant-bearing levels were studied. A vegetation change is recorded in the fossil level bearing Agathoxylon argentinum n. sp., marked by the replacement of the corystosperm genera and a diminution of arboreal corystosperms. This floristic change, in addition to other evidence, indicates humid paleoclimatic conditions for the uppermost part of the Valle de La Luna Member of the Ischigualasto Formation.
Cumulative environmental risk in early life is associated with mental disorders in childhood
Authors: O'Hare Kirstie , Watkeys Oliver , Whitten Tyson , Dean Kimberlie , Laurens Kristin R. , Harris Felicity , Carr Vaughan J. , Green Melissa J. 
Published: July 2022

AbstractBackgroundNo single environmental factor is a necessary or sufficient cause of mental disorder; multifactorial and transdiagnostic approaches are needed to understand the impact of the environment on the development of mental disorders across the life course.MethodUsing linked multi-agency administrative data for 71 932 children from the New South Wales Child Developmental Study, using logistic regression, we examined associations between 16 environmental risk factors in early life (prenatal period to <6 years of age) and later diagnoses of mental disorder recorded in health service data (from age 6 to 13 years), both individually and summed as an environmental risk score (ERS).ResultsThe ERS was associated with all types of mental disorder diagnoses in a dose–response fashion, such that 2.8% of children with no exposure to any of the environmental factors (ERS = 0), compared to 18.3% of children with an ERS of 8 or more indicating exposure to 8 or more environmental factors (ERS ⩾ 8), had been diagnosed with any type of mental disorder up to age 13–14 years. Thirteen of the 16 environmental factors measured (including prenatal factors, neighbourhood characteristics and more proximal experiences of trauma or neglect) were positively associated with at least one category of mental disorder.ConclusionExposure to cumulative environmental risk factors in early life is associated with an increased likelihood of presenting to health services in childhood for any kind of mental disorder. In many instances, these factors are preventable or capable of mitigation by appropriate public policy settings.
Coordination frictions and economic growth
Authors: Gabrovski Miroslav 
Published: July 2022

AbstractIn practice, firms face a number of scarce innovation projects. They choose one towards which to direct their effort, but do not coordinate these choices. This gives rise to coordination frictions. This paper develops an expanding-variety endogenous growth model to study the implications of these frictions for growth and welfare. We find that the coordination failure generates a number of foregone innovations and reduces the economy-wide research intensity. Both effects decrease the growth rate. This creates a general equilibrium effect that endogenously amplifies the fraction of wasteful simultaneous innovation. Furthermore, formalizing the coordination frictions uncovers a novel link between the “stepping on toes” and “standing on shoulders” externalities—their magnitudes are endogenously determined through the ratio of firms to innovation projects. We find that the “stepping on toes” externality is larger for all parameter values.
Analyzing Semantics of Aggregate Answer Set Programming Using Approximation Fixpoint Theory
Authors: VANBESIEN LINDE , BRUYNOOGHE MAURICE , DENECKER MARC 
Published: July 2022

AbstractAggregates provide a concise way to express complex knowledge. The problem of selecting an appropriate formalization of aggregates for answer set programming (ASP) remains unsettled. This paper revisits it from the viewpoint of Approximation Fixpoint Theory (AFT). We introduce an AFT formalization equivalent with the Gelfond–Lifschitz reduct for basic ASP programs and we extend it to handle aggregates. We analyze how existing approaches relate to our framework. We hope this work sheds some new light on the issue of a proper formalization of aggregates.
Ten misconceptions about trauma-focused CBT for PTSD
Authors: Murray Hannah , Grey Nick , Warnock-Parkes Emma , Kerr Alice , Wild Jennifer , Clark David M. , Ehlers Anke 
Published: July 2022

AbstractTherapist cognitions about trauma-focused psychological therapies can affect our implementation of evidence-based therapies for post-traumatic stress disorder (PTSD), potentially reducing their effectiveness. Based on observations gleaned from teaching and supervising one of these treatments, cognitive therapy for PTSD (CT-PTSD), ten common ‘misconceptions’ were identified. These included misconceptions about the suitability of the treatment for some types of trauma and/or emotions, the need for stabilisation prior to memory work, the danger of ‘retraumatising’ patients with memory-focused work, the risks of using memory-focused techniques with patients who dissociate, the remote use of trauma-focused techniques, and the perception of trauma-focused CBT as inflexible. In this article, these misconceptions are analysed in light of existing evidence and guidance is provided on using trauma-focused CT-PTSD with a broad range of presentations.Key learning aims(1)To recognise common misconceptions about trauma-focused CBT for PTSD and the evidence against them.(2)To widen understanding of the application of cognitive therapy for PTSD (CT-PTSD) to a broad range of presentations.(3)To increase confidence in the formulation-driven, flexible, active and creative delivery of CT-PTSD.
Overall survival in the SIMPLIFY-1 and SIMPLIFY-2 phase 3 trials of momelotinib in patients with myelofibrosis
Authors: Mesa Ruben , Harrison Claire , Oh Stephen T. , Gerds Aaron T. , Gupta Vikas , Catalano John , Cervantes Francisco , Devos Timothy , Hus Marek , Kiladjian Jean-Jacques , Lech-Maranda Ewa , McLornan Donal , Vannucchi Alessandro M. , Platzbecker Uwe , Huang Mei , Strouse Bryan , Klencke Barbara , Verstovsek Srdan 
Published: July 2022

AbstractJanus kinase inhibitors (JAKi) approved for myelofibrosis provide spleen and symptom improvements but do not address anemia, a negative prognostic factor. Momelotinib, an inhibitor of ACVR1/ALK2, JAK1 and JAK2, demonstrated activity against anemia, symptoms, and splenomegaly in the phase 3 SIMPLIFY trials. Here, we report mature overall survival (OS) and leukemia-free survival (LFS) from both studies, and retrospective analyses of baseline characteristics and efficacy endpoints for OS associations. Survival distributions were similar between JAKi-naïve patients randomized to momelotinib, or ruxolitinib then momelotinib, in SIMPLIFY-1 (OS HR = 1.02 [0.73, 1.43]; LFS HR = 1.08 [0.78, 1.50]). Two-year OS and LFS were 81.6% and 80.7% with momelotinib and 80.6% and 79.3% with ruxolitinib then momelotinib. In ruxolitinib-exposed patients in SIMPLIFY-2, two-year OS and LFS were 65.8% and 64.2% with momelotinib and 61.2% and 59.7% with best available therapy then momelotinib (OS HR = 0.98 [0.59, 1.62]; LFS HR = 0.97 [0.59, 1.60]). Baseline transfusion independence (TI) was associated with improved survival in both studies (SIMPLIFY-1 HR = 0.474, p = 0.0001; SIMPLIFY-2 HR = 0.226, p = 0.0005). Week 24 TI response in JAKi-naïve, momelotinib-randomized patients was associated with improved OS in univariate (HR = 0.323; p < 0.0001) and multivariate (HR = 0.311; p < 0.0001) analyses. These findings underscore the importance of achieving or maintaining TI in myelofibrosis, supporting the clinical relevance of momelotinib’s pro-erythropoietic mechanism of action, and potentially informing treatment decision-making.
Seed-induced Aβ deposition alters neuronal function and impairs olfaction in a mouse model of Alzheimer’s disease
Authors: Ziegler-Waldkirch Stephanie , Friesen Marina , Loreth Desirée , Sauer Jonas-Frederic , Kemna Solveig , Hilse Alexandra , Erny Daniel , Helm Christina , d´Errico Paolo , Prinz Marco , Bartos Marlene , Meyer-Luehmann Melanie 
Published: July 2022

AbstractAlzheimer’s disease (AD) is characterized by the accumulation of amyloid-β (Aβ) which ultimately forms plaques. These Aβ deposits can be induced in APP transgenic mouse models by prion-like seeding. It has been widely accepted that anosmia and hyposmia occur during the early stages of AD, even before cognitive deficits are present. In order to determine the impact of seed-induced Aβ deposits on olfaction, we performed intracerebral injections of seed-competent brain homogenate into the olfactory bulb of young pre-depositing APP transgenic mice. Remarkably, we observed a dramatic olfactory impairment in those mice. Furthermore, the number of newborn neurons as well as the activity of cells in the mitral cell layer was decreased. Notably, exposure to an enriched environment reduced Aβ seeding, vivified neurogenesis and most importantly reversed olfactory deficits. Based on our findings, we conclude that altered neuronal function as a result of induced Aβ pathology might contribute to olfactory dysfunction in AD.
A blockchain-based framework to support pharmacogenetic data sharing
Authors: Albalwy F. , McDermott J. H. , Newman W. G. , Brass A. , Davies A. 
Published: July 2022

AbstractThe successful implementation of pharmacogenetics (PGx) into clinical practice requires patient genomic data to be shared between stakeholders in multiple settings. This creates a number of barriers to widespread adoption of PGx, including privacy concerns related to the storage and movement of identifiable genomic data. Informatic solutions that support secure and equitable data access for genomic data are therefore important to PGx. Here we propose a methodology that uses smart contracts implemented on a blockchain-based framework, PGxChain, to address this issue. The design requirements for PGxChain were identified through a systematic literature review, identifying technical challenges and barriers impeding the clinical implementation of pharmacogenomics. These requirements included security and privacy, accessibility, interoperability, traceability and legal compliance. A proof-of-concept implementation based on Ethereum was then developed that met the design requirements. PGxChain’s performance was examined using Hyperledger Caliper for latency, throughput, and transaction success rate. The findings clearly indicate that blockchain technology offers considerable potential to advance pharmacogenetic data sharing, particularly with regard to PGx data security and privacy, large-scale accessibility of PGx data, PGx data interoperability between multiple health care providers and compliance with data-sharing laws and regulations.
Gastrointestinal cancer-associated fibroblasts expressing Junctional Adhesion Molecule-A are amenable to infection by oncolytic reovirus
Authors: Harryvan Tom J. , Golo Matteo , Dam Nicole , Schoonderwoerd Mark J. A. , Farshadi Elham Aida , Hornsveld Marten , Hoeben Rob C. , Hawinkels Lukas J. A. C. , Kemp Vera 
Published: July 2022

AbstractGastrointestinal (GI) cancers are characterized by extensive tumor stroma that both promotes tumor progression and acts as a physical barrier for adjacent tumor cells, limiting the effect of current treatment modalities. Oncolytic virotherapy is currently investigated in clinical trials as a novel therapeutic agent for different malignancies of the GI tract, but it is largely unknown whether these viruses can also target the tumor stroma. Here, we investigated the tropism of two commonly studied OVs, adenovirus and reovirus, towards primary GI fibroblasts from human oesophageal, gastric, duodenal and pancreatic carcinomas (N = 36). GI fibroblasts were susceptible to type 3 Dearing (T3D) strain R124 and bioselected mutant reovirus (jin-3) infection but not oncolytic adenovirus (Ad5-Δ24). Efficient infection and apoptosis of human and mouse GI cancer-derived fibroblasts by these reoviruses was partially dependent on the expression of the reovirus entry receptor, Junctional Adhesion Molecule-A (JAM-A). Moreover, human GI cancer organoid-fibroblast co-cultures showed higher overall infectivity when containing JAM-A expressing fibroblasts as compared to JAM-A negative fibroblasts, indicating a potential role of JAM-A expressing fibroblasts for viral dissemination. We further show that JAM-A is not only necessary for efficient reovirus infection of fibroblasts but also partially mediates reovirus-induced apoptosis, dependent on signaling through the C-terminal PDZ-domain of JAM-A. Altogether, our data show the presence of JAM-A expressing fibroblasts in both human and murine GI cancers that are amenable to infection and induction of apoptosis by reovirus, extending the potential anti-cancer actions of reovirus with stromal targeting.
SARM1 deletion in parvalbumin neurons is associated with autism-like behaviors in mice
Authors: Xiang Ludan , Wu Qian , Sun Huankun , Miao Xuemeng , Lv Zhaoting , Liu Huitao , Chen Lan , Gu Yanrou , Chen Jianjun , Zhou Siyao , Jiang Huixia , Du Siyu , Zhou Yixin , Dong Hui , Fan Yiren , Miao Shuangda , Lu Qi , Chang Liyun , Wang Hui , Lu Yi , Xu Xingxing , Wang Wei , Huang Zhihui 
Published: July 2022

AbstractAutism spectrum disorder (ASD), a group of neurodevelopmental disorder diseases, is characterized by social deficits, communication difficulties, and repetitive behaviors. Sterile alpha and TIR motif-containing 1 protein (SARM1) is known as an autism-associated protein and is enriched in brain tissue. Moreover, SARM1 knockdown mice exhibit autism-like behaviors. However, its specific mechanism in ASD pathogenesis remains unclear. Here we generated parvalbumin-positive interneurons (PVI)-specific conditional SARM1 knockout (SARM1PV-CKO) mice. SARM1PV-CKO male mice showed autism-like behaviors, such as mild social interaction deficits and repetitive behaviors. Moreover, we found that the expression level of parvalbumin was reduced in SARM1PV-CKO male mice, together with upregulated apoptosis-related proteins and more cleaved-caspase-3-positive PVIs, suggesting that knocking out SARM1 may cause a reduction in the number of PVIs due to apoptosis. Furthermore, the expression of c-fos was shown to increase in SARM1PV-CKO male mice, in combination with upregulation of excitatory postsynaptic proteins such as PSD-95 or neuroligin-1, indicating enhanced excitatory synaptic input in mutant mice. This notion was further supported by the partial rescue of autism-like behavior deficits by the administration of GABA receptor agonists in SARM1PV-CKO male mice. In conclusion, our findings suggest that SARM1 deficiency in PVIs may be involved in the pathogenesis of ASD.
Merging of relaxations and step-like increase of accompanying supercooled liquid region in metallic glasses via ultrafast nanocalorimetry
Authors: Gao Meng , Perepezko John H. 
Published: July 2022

AbstractGlassy materials under external stimuli usually display multiple and complex relaxations. The relaxations and the evolution paths of glassy materials significantly affect their properties and are closely related to many key issues in glass physics, such as glass transition and thermoplastic forming. However, until now, the relaxation dynamics in the presence of external stimuli and the microscopic atomic motion of glassy materials have been unclear due to the lack of structural information. By combining Flash and conventional differential scanning calorimetry (DSC), we applied a very large range of heating rate of six orders of magnitude and investigated the relaxation dynamics of three typical metallic glasses. We discovered the merging of distinct relaxation events with increasing rate of heating. Most interestingly, the experiments revealed new behaviors with step-like increases in the supercooled liquid region and excess heat capacity during the merging of multiple relaxations. A comprehensive scheme was proposed for the evolution of the thermal relaxation spectrum, the heterogeneity of the corresponding atomic motion and the potential energy landscape with rate of heating. These experimental results shed light on the mechanism of atomic rearrangement during heating and provided a new approach to regulate the physical properties of amorphous materials by controlling their intrinsic relaxation dynamics.