bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting microbiomes through a deep latent space
Authors: García-Jiménez Beatriz , Muñoz Jorge , Cabello Sara , Medina Joaquín , Wilkinson Mark D 
Published: November 2020

Abstract

Motivation
Microbial communities influence their environment by modifying the availability of compounds, such as nutrients or chemical elicitors. Knowing the microbial composition of a site is therefore relevant to improve productivity or health. However, sequencing facilities are not always available, or may be prohibitively expensive in some cases. Thus, it would be desirable to computationally predict the microbial composition from more accessible, easily-measured features.

Results
Integrating deep learning techniques with microbiome data, we propose an artificial neural network architecture based on heterogeneous autoencoders to condense the long vector of microbial abundance values into a deep latent space representation. Then, we design a model to predict the deep latent space and, consequently, to predict the complete microbial composition using environmental features as input. The performance of our system is examined using the rhizosphere microbiome of Maize. We reconstruct the microbial composition (717 taxa) from the deep latent space (10 values) with high fidelity (&gt;0.9 Pearson correlation). We then successfully predict microbial composition from environmental variables, such as plant age, temperature or precipitation (0.73 Pearson correlation, 0.42 Bray–Curtis). We extend this to predict microbiome composition under hypothetical scenarios, such as future climate change conditions. Finally, via transfer learning, we predict microbial composition in a distinct scenario with only 100 sequences, and distinct environmental features. We propose that our deep latent space may assist microbiome-engineering strategies when technical or financial resources are limited, through predicting current or future microbiome compositions.

Availability and implementation
Software, results and data are available at https://github.com/jorgemf/DeepLatentMicrobiome

Supplementary information
Supplementary data are available at Bioinformatics online.
Sedentary behaviour in the workplace: prevalence, health implications and interventions
Authors: Bailey Daniel P 
Published: November 2020

Abstract

Introduction
This paper reviews the prevalence and health risks of excess sedentary behaviour in office workers, and the effectiveness of sedentary workplace interventions in a manner accessible to practitioners.

Sources of data
A narrative review of empirical studies obtained from PubMed and Web of Science.

Areas of agreement
Office workers are highly sedentary, increasing their risk of health problems. Interventions using individual, organisational and environmental level strategies can be effective for reducing workplace sitting.

Areas of controversy
The effects of sedentary workplace interventions on health are inconsistent. This may be due to a lack of randomized controlled trials powered to detect changes in health outcomes.

Growing points
Multicomponent interventions that use a combination of the strategies above may be the most effective for reducing sitting.

Areas timely for developing research
Determining the long-term health and cost-effectiveness of sedentary workplace interventions is a priority to encourage employer buy-in for their implementation.
Randomized, Double-Blinded, Placebo-Controlled Phase 2 Trial of an Inactivated Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine in Healthy Adults
Authors: Che Yanchun , Liu Xiaoqiang , Pu Yi , Zhou Meijian , Zhao Zhimei , Jiang Ruiju , Yin Zhifang , Xu Mingjue , Yin Qiongzhou , Wang Jianfeng , Pu Jing , Zhao Heng , Zhang Ying , Wang Lichun , Jiang Ya , Lei Jin , Zheng Yan , Liao Yun , Long Runxiang , Yu Li , Cui Pingfang , Yang Huijuan , Zhang Yuehui , Li Jingyu , Chen Weiwu , He Zhanlong , Ma Kaili , Hong Chao , Li Dandan , Jiang Guorun , Liu Donglan , Xu Xingli , Fan Shengtao , Cheng Chen , Zhao Hongling , Yang Jianbo , Li Yan , Zou Yanxiang , Zhu Youshuai , Zhou Yaling , Guo Yingqiu , Yang Ting , Chen Hongbo , Xie Zhongping , Li Changgui , Li Qihan 
Published: November 2020

Abstract

Background
We evaluated an inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine for immunogenicity and safety in adults aged 18–59 years.

Methods
In this randomized, double-blinded, controlled trial, healthy adults received a medium dose (MD) or a high dose (HD) of the vaccine at an interval of either 14 days or 28 days. Neutralizing antibody (NAb) and anti-S and anti-N antibodies were detected at different times, and adverse reactions were monitored for 28 days after full immunization.

Results
A total of 742 adults were enrolled in the immunogenicity and safety analysis. Among subjects in the 0, 14 procedure, the seroconversion rates of NAb in MD and HD groups were 89% and 96% with geometric mean titers (GMTs) of 23 and 30, respectively, at day 14 and 92% and 96% with GMTs of 19 and 21, respectively, at day 28 after immunization. Anti-S antibodies had GMTs of 1883 and 2370 in the MD group and 2295 and 2432 in the HD group. Anti-N antibodies had GMTs of 387 and 434 in the MD group and 342 and 380 in the HD group. Among subjects in the 0, 28 procedure, seroconversion rates for NAb at both doses were both 95% with GMTs of 19 at day 28 after immunization. Anti-S antibodies had GMTs of 937 and 929 for the MD and HD groups, and anti-N antibodies had GMTs of 570 and 494 for the MD and HD groups, respectively. No serious adverse events were observed during the study period.

Conclusions
Adults vaccinated with inactivated SARS-CoV-2 vaccine had NAb as well as anti-S/N antibody and had a low rate of adverse reactions.

Clinical Trials Registration
NCT04412538.
Sensitivity of C-Reactive Protein and Procalcitonin Measured by Point-of-Care Tests to Diagnose Urinary Tract Infections in Nursing Home Residents: A Cross-Sectional Study
Authors: Kuil S D , Hidad S , Fischer J C , Harting J , Hertogh C M P M , Prins J M , de Jong M D , van Leth F , Schneeberger C 
Published: November 2020

Abstract

Background
Diagnosing urinary tract infections (UTIs) in nursing home residents is complex, as specific urinary symptoms are often absent and asymptomatic bacteriuria (ASB) is prevalent. The aim of this study was to assess the sensitivity of blood C-reactive protein (CRP) and procalcitonin (PCT), measured by point-of-care tests (PoCTs), to diagnose UTIs in this setting.

Methods
Elderly residents (≥65 years old) with a suspected UTI were recruited from psychogeriatric, somatic, or rehabilitation wards across 13 participating nursing homes. CRP and PCT were tested simultaneously in the same study participants. To assess the tests’ sensitivities, a stringent definition of “true” UTI was used that included the presence of symptoms, urinary leucocytes, a positive urine culture, and symptom resolution during antibiotic treatment covering isolated uropathogen(s). The original sample size was 440 suspected UTI episodes, in order to detect a clinically relevant sensitivity of at least 65% when calculated using the matched analysis approach to compare both PoCTs.

Results
After enrollment of 302 episodes (68.6% of the planned sample size), an unplanned and funder-mandated interim analysis was done, resulting in premature discontinuation of the study for futility. For 247 of 266 eligible episodes, all mandatory items required for the true UTI definition (92.9%) were available. In total, 49 episodes fulfilled our stringent UTI definition (19.8%). The sensitivities of CRP (cut-off, 6.5 mg/L) and PCT (cut-off, 0.025 ng/mL) were 52.3% (95% confidence interval [CI], 36.7–67.5%) and 37.0% (95% CI, 23.2–52.5%), respectively.

Conclusions
Our results indicate that CRP and PCT are not suitable tests for distinguishing UTI and ASB in nursing home residents.

Clinical Trials Registration
Netherlands Trial Registry NL6293.
Wild-type transthyretin amyloid cardiomyopathy complicated by spinal canal stenosis, carpal tunnel syndrome, and rotator cuff tears: a case report
Authors: Takashio Seiji , Nishi Masato , Tsuruta Yuichiro , Tsujita Kenichi 
Published: November 2020

Abstract

Background
Wild-type transthyretin amyloid cardiomyopathy (ATTRwt-CM) is receiving increasing attention due to the availability of novel treatment options. Carpal tunnel syndrome (CTS) and lumbar spinal canal stenosis are known early symptoms of transthyretin (TTR) amyloidosis preceding the cardiac involvement and are considered as ‘Red Flags’ for transthyretin amyloid cardiomyopathy (ATTR-CM).

Case summary
A 67-year-old man with a history of lumbar spinal canal stenosis for the last 10 years, right rotator cuff tears for the last 4 years, and bilateral CTS for the last 1 year was scheduled for orthopaedic surgery for lumbar spinal canal stenosis. Investigations revealed severe left ventricular hypertrophy and hypertroponinaemia, which were suggestive of cardiac amyloidosis. Cardiac magnetic resonance imaging and 99mTc-labelled pyrophosphate scintigraphy demonstrated positive findings for ATTR-CM. Transthyretin deposition was found in both the myocardium and the yellow ligamentum excised during surgery. There was no transthyretin mutation on genetic testing. The final diagnosis was ATTRwt-CM.

Discussion
Transthyretin deposition in the ligaments or tendons has been observed in a number of patients with CTS, spinal canal stenosis, and rotator cuff tears. These orthopaedic diseases are predictive for the future occurrence of ATTR-CM. In addition, the coexistence of these multiple diseases might strongly predict ATTR-CM. This knowledge needs to be shared with orthopaedicians and cardiologists for the early diagnosis of ATTR-CM.
Multilayer bare stent technique in treating intact mycotic suprarenal aortic aneurysm: a case report
Authors: Song Chao , Cai Qing , Huang Yi , Lu Qingsheng 
Published: November 2020

Abstract

Background
Invasive aspergillosis (IA) related mycotic aortic aneurysm is rare in immunocompetent patient. The endovascular therapy remains controversial due to potential risk of graft infection, while the suprarenal cases might face catastrophic complications during open surgery.

Case summary
We presented an IA case with suprarenal abdominal aortic aneurysm confirmed by joint effusion. Multilayer bare stent technique was performed to preserve visceral blood flow and promote aneurysmal thrombus formation, along with antifungal treatment. Two years of follow-up revealed complete aneurysm thrombosis without evidence of infection.

Discussion
Fungal infection that affects the aorta is difficult to recognize due to often negative blood cultures. Close observation is recommended in case of suspicion of mycotic aneurysms. Multilayer bare stent technique can restore luminal laminar blood flow and reduce the risk of infection in intact mycotic suprarenal aortic aneurysm.
Corynebacterium jeikeium native valve infective endocarditis case report: a confirmed microbiological and pathological diagnosis from heart valvular tissue
Authors: Dowling Wentzel Bruce , Koen Johan 
Published: November 2020

Abstract

Background
The Modified Duke criteria is an important structured schematic for the diagnosis of infective endocarditis (IE). Corynebacterium jeikeium is a rare cause of IE that is often resistant to standard IE anti-microbials. We present a case of C. jeikeium IE, fulfilling the Modified Duke pathological criteria.

Case summary
A 50-year-old male presented with left leg peripheral vascular disease with septic changes requiring amputation. Routine echocardiography post-amputation demonstrated severe aortic valve regurgitation with vegetations that required valve replacement. Two initial blood cultures from a single venepuncture showed Streptococcus mitis which was treated with penicillin G prior to surgery. Subsequent aortic valve tissue cultured C. jeikeium with suggestive IE histological valvular changes and was successfully treated on a prolonged course of vancomycin.

Discussion
This is the first C. jeikeium IE case diagnosed on heart valvular tissue culture and highlights the importance for the fulfilment of the Modified Duke criteria in diagnosing left-sided IE. Mixed infection IE is rare, and this case possibly represents an unmasking of resistant C. jeikeium IE following initial treatment of penicillin G.
A case report of advanced heart failure refractory to pharmacological therapy who was successfully recovered by combinatory usage of cardiac resynchronizing therapy, Impella and MitraClip
Authors: Sobajima Mitsuo , Fukuda Nobuyuki , Ueno Hiroshi , Kinugawa Koichiro 
Published: November 2020

Abstract

Background
The safety and efficacy of MitraClip for advanced heart failure (HF) patients who are inotrope-dependent or mechanically supported are unknown.

Case summary
The patient was a 71-year-old man diagnosed as dilated cardiomyopathy in 2003. He was admitted due to worsening HF in January 2019 and became dependent upon intravenous infusion of inotropes. During the 8-month hospitalization, his haemodynamics were relatively static with bed rest and continuous inotropes, but he was definitely dependent on them. Our multidisciplinary team decided to perform both cardiac resynchronization therapy (CRT) and MitraClip under Impella support. First, Impella was inserted from left subclavian artery. After a week, CRT was implanted from right subclavian vein, and the QRS duration of electrocardiogram became remarkably narrow. MitraClip was performed 2 weeks after Impella, and functional mitral regurgitation improved from severe to mild, and Impella was removed on the same day. Inotropes could be ceased, and he was discharged 2 months after MitraClip.

Discussion
During inotrope-dependent status, there was a risk that HF would worsen with haemodynamic collapse when performing CRT implantation, and we firstly supported his haemodynamics by Impella. Cardiac resynchronization therapy implantation before MitraClip seemed to be crucial. In fact, the mitral valve morphology before Impella insertion had very poor coaptation of the anterior and posterior leaflets that was not optimal for MitraClip procedure. But the Impella support and correction of dyssynchrony by CRT markedly improved the coaptation of those leaflets. The combination therapy of CRT and MitraClip unloading with Impella maybe a new therapeutic option for advanced HF.
How and Why Was Domesday Made?
Authors: Baxter Stephen 
Published: November 2020

Abstract
This article offers a new interpretation of the Domesday survey, drawing upon a collaborative study of its earliest surviving manuscript, Exeter Cathedral Library MS 3500 (Exon). It identifies five principal stages: first, the survey was launched at Gloucester in midwinter 1085; secondly, fiscal information extracted from geld assessment lists was integrated with manorial detail supplied by landholders to create a survey organised on a geographical plan by hundred; thirdly, this hundredal recension was checked by a second group of commissioners at meetings of shire courts, generating a substantial corpus of contested matter; fourthly, the hundredal recension was restructured into circuit returns which grouped together and summarised the holdings of barons who held directly from the king; fifthly, Domesday Book itself was written directly from these circuit returns. Royal assemblies held at Easter, Whitsun and Lammas functioned as deadlines for the second, third and fourth stages respectively; and a major geld levied at the rate of six shillings to the hide was collected and accounted for during this period. The survey generated a range of different outputs, each intended to serve specific fiscal and political purposes: the hundredal recension was designed to facilitate a reassessment of geld liabilities; the lists of contested matter anticipated a later judicial review; the circuit returns, summaries and Domesday Book were designed to make the administration of the royal demesne and the profits of royal lordship more efficient. The latter also supplied barons with what amounted to confirmation charters of their uncontested holdings, for which they performed homage.
Mantle dynamics of the Andean Subduction Zone from continent-scale teleseismic S-wave tomography
Authors: Rodríguez Emily E , Portner Daniel Evan , Beck Susan L , Rocha Marcelo P , Bianchi Marcelo B , Assumpção Marcelo , Ruiz Mario , Alvarado Patricia , Condori Cristobal , Lynner Colton 
Published: November 2020

SUMMARY
The Andean Subduction Zone is one of the longest continuous subduction zones on Earth. The relative simplicity of the two-plate system has makes it an ideal natural laboratory to study the dynamics in subduction zones. We measure teleseismic S and SKS traveltime residuals at &gt;1000 seismic stations that have been deployed across South America over the last 30 yr to produce a finite-frequency teleseismic S-wave tomography model of the mantle beneath the Andean Subduction Zone related to the Nazca Plate, spanning from ∼5°N to 45°S and from depths of ∼130 to 1200 km. Within our model, the subducted Nazca slab is imaged as a fast velocity seismic anomaly. The geometry and amplitude of the Nazca slab anomaly varies along the margin while the slab anomaly continues into the lower mantle along the entirety of the subduction margin. Beneath northern Brazil, the Nazca slab appears to stagnate at ∼1000 km depth and extend eastward subhorizontally for &gt;2000 km. South of 25°S the slab anomaly in the lower mantle extends offshore of eastern Argentina, hence we do not image if a similar stagnation occurs. We image several distinct features surrounding the slab including two vertically oriented slow seismic velocity anomalies: one beneath the Peruvian flat slab and the other beneath the Paraná Basin of Brazil. The presence of the latter anomaly directly adjacent to the stagnant Nazca slab suggests that the plume, known as the Paraná Plume, may be a focused upwelling formed in response to slab stagnation in the lower mantle. Additionally, we image a high amplitude fast seismic velocity anomaly beneath the Chile trench at the latitude of the Sierras Pampeanas which extends from ∼400 to ∼1000 km depth. This anomaly may be the remnants of an older, detached slab, however its relationship with the Nazca–South America subduction zone remains enigmatic.
Delivery Outcomes of Pregnant Patients With Inflammatory Bowel Diseases Compared With the General Population and With Women With Other Autoimmune Diseases at a Tertiary Care Center
Authors: Geisman Taylor , Chen Ling , Gray-Swain Margaret Rosanna , Hiatt-Jensen Deborah , Gutierrez Alexandra 
Published: November 2020

Abstract

Background
Variable data have suggested that pregnant women with inflammatory bowel diseases (IBD) are more likely to have cesarean deliveries and adverse pregnancy outcomes than the general population. The aim of this study was to describe the rates of cesarean delivery and adverse pregnancy outcomes among patients with IBD as compared with patients with other autoimmune diseases and with the general population.

Methods
Pregnant patients with IBD, those with non-IBD autoimmune diseases, and control patients were identified. Baseline demographics, disease characteristics, medication use, and delivery outcomes were recorded in a retrospective manner. The primary outcome was overall rate of cesarean delivery; secondary outcomes included rates of planned and unplanned cesarean delivery, delivery complications, preterm delivery, and fetal complications.

Results
Ninety-three women with IBD were age-matched to 376 control patients; 38 women with other autoimmune diseases were also identified. Women with IBD had higher rates of cesarean delivery (47%) when compared with control patients (31%; P &lt; 0.0001) but not when compared with women with other autoimmune diseases. There were high rates of planned cesarean deliveries for IBD-related factors in the IBD cohort. Women with IBD did not have increased rates of adverse delivery or fetal outcomes.

Conclusions
Women with IBD have higher rates of cesarean delivery than the general population and rates similar to those of women with other autoimmune diseases. Planned cesarean delivery plays an important role in maintaining continuity and sphincter control in select situations, but a diagnosis of IBD does not mandate cesarean delivery.
The causes and consequences of a judicialized peace process in Colombia
Authors: Landau David 
Published: November 2020

Abstract
This article focuses on one striking feature of the Colombian peace process with the Revolutionary Armed Forces of Colombia—People’s Army (FARC): a very high level of judicialization, as shown through the many decisions issued by the Colombian Constitutional Court that have examined core elements of the process. It argues that this high level of judicialization is explained not only by the generally activist role conception of the Court, but also by specific doctrines it developed, including a robust incorporation of international law and an unconstitutional constitutional amendment doctrine, which essentially made judicialization inevitable. Since these doctrinal devices are spreading, they may portend increasingly judicialized peace processes in other countries as well. Normatively, judicialization of ongoing peace processes raises clear risks, particularly of destabilization. But for the most part, the Colombian Constitutional Court has avoided these risks and instead has stabilized the process in important ways, by insulating it from both international pressure and domestic political shifts. The Court has also injected important values into the process, especially regarding the rights of victims of the internal armed conflict. Thus, the case study demonstrates that at least under certain conditions, judicialization may have a beneficial impact on the substance and durability of peace processes.
Kinematic constraints on spatial curvature from supernovae Ia and cosmic chronometers
Authors: Jesus J F , Valentim R , Moraes P H R S , Malheiro M 
Published: November 2020

ABSTRACT
An approach to estimate the spatial curvature Ωk from data independently of dynamical models is suggested, through kinematic parametrizations of the comoving distance [DC(z)] with third-degree polynomial, of the Hubble parameter [H(z)] with a second-degree polynomial and of the deceleration parameter [q(z)] with first-order polynomial. All these parametrizations were done as function of redshift z. We used SNe Ia data set from Pantheon compilation with 1048 distance moduli estimated in the range 0.01 &lt; z &lt; 2.3 with systematic and statistical errors and a compilation of 31 H(z) data estimated from cosmic chronometers. The spatial curvature found for DC(z) parametrization was $\Omega _{k}=-0.03^{+0.24+0.56}_{-0.30-0.53}$. The parametrization for deceleration parameter q(z) resulted in $\Omega _{k}=-0.08^{+0.21+0.54}_{-0.27-0.45}$. The H(z) parametrization has shown incompatibilities between H(z) and SNe Ia data constraints, so these analyses were not combined. The DC(z) and q(z) parametrizations are compatible with the spatially flat universe as predicted by many inflation models and data from cosmic microwave background. This type of analysis is very appealing as it avoids any bias because it does not depend on assumptions about the matter content of the Universe for estimating Ωk.
On the growth of the thermally modified non-resonant streaming instability
Authors: Marret A , Ciardi A , Smets R , Fuchs J 
Published: November 2020

ABSTRACT
The cosmic rays non-resonant streaming instability is believed to be the source of substantial magnetic field amplification. In this work, we investigate the effects of the ambient plasma temperature on the instability and derive analytical expressions of its growth rate in the hot, demagnetized regime of interaction. To study its non-linear evolution, we perform hybrid-PIC simulations for a wide range of temperatures. We find that in the cold limit, about two-thirds of the cosmic rays drift kinetic energy is converted into magnetic energy. Increasing the temperature of the ambient plasma can substantially reduce the growth rate and the magnitude of the saturated magnetic field.