bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a novel type of glucose dehydrogenase involved in the mineral weathering ability of Collimonas pratensis strain PMB3(1)
Authors: Picard L , Turpault M-P , Oger P M , Uroz S 
Published: November 2020

Abstract
The exact molecular mechanisms as well as the genes involved in the mineral weathering (MW) process by bacteria remain poorly characterized. To date, a single type of glucose dehydrogenase (GDH) depending on a particular co-factor named pyrroloquinoline quinone (PQQ) is known. These enzymes allow the production of gluconic acid through the oxidation of glucose. However, it remains to be determined how bacteria missing PQQ-dependent GDH and/or the related pqq biogenesis genes weather minerals. In this study, we considered the very effective mineral weathering bacterial strain PMB3(1) of Collimonas pratensis. Genome analysis revealed that it does not possess the PQQ based system. The use of random mutagenesis, gene complementation and functional assays allowed us to identify mutants impacted in their ability to weather mineral. Among them, three mutants were strongly altered on their acidification and biotite weathering abilities (58 to 75% of reduction compared to WT) and did not produce gluconic acid. The characterization of the genomic regions allowed noticeably to the identification of a Glucose/Methanol/Choline oxidoreductase. This region appeared very conserved among collimonads and related genera. This study represents the first demonstration of the implication of a PQQ-independent GDH in the mineral weathering process and explains how Collimonas weather minerals.
LisRK is required for optimal fitness ofListeria monocytogenesin soil
Authors: Brunhede Maja Z , Santos Patrícia T Dos , Gal Laurent , Garmyn Dominique , Kallipolitis Birgitte H , Piveteau Pascal 
Published: November 2020

ABSTRACTListeria monocytogenes is a food-borne pathogen responsible for the disease listeriosis. It is ubiquitously found in the environment and soil is one of its natural habitats. Listeria monocytogenes is highly capable of coping with various stressful conditions. We hypothesized that stress-responsive two-component systems such as LisRK might contribute to the adaptation of L. monocytogenes to the soil environment. Indeed, investigations of the population dynamics of wild-type and mutant strains suggest an important role of LisRK for optimal fitness of L. monocytogenes in sterile soil. Results from non-sterile soil showed that the parental strain was capable of surviving longer than mutant strains lacking lisRK or genes encoding the LisRK-regulated LhrC small RNAs (sRNAs), suggesting that LisRK as well as the LhrC sRNAs were important for survival. Transcription of five LisRK-regulated genes was assessed after 1 h incubation in sterile soil. We observed that LisRK and the LhrC sRNAs contribute to the upregulation of lmo2522 in the soil environment. Notably, lmo2522 encodes an equivalent of the resuscitation promoting factors, Rpfs, in actinobacteria. Collectively, our study demonstrates that LisRK is important for growth and survival in sterile and non-sterile soil and suggests a role for LisRK-regulation of Lmo2522 in resuscitation from dormancy in the soil environment.
Cross-Sectional and Longitudinal Associations Between Plasma Neurodegenerative Biomarkers and Physical Performance Among Community-Dwelling Older Adults
Authors: He Lingxiao , de Souto Barreto Philipe , Giudici Kelly V , Aggarwal Geetika , Nguyen Andrew D , Morley John E , Li Yan , Bateman Randall J , Vellas Bruno ,   for the MAPT/DSA Group, Vellas Bruno , Guyonnet Sophie , Carrié Isabelle , Brigitte Lauréane , Faisant Catherine , Lala Françoise , Delrieu Julien , Villars Hélène , Combrouze Emeline , Badufle Carole , Zueras Audrey , Andrieu Sandrine , Cantet Christelle , Morin Christophe , Abellan Van Kan Gabor , Dupuy Charlotte , Rolland Yves , Caillaud Céline , Ousset Pierre-Jean , Lala Françoise 
Published: November 2020

Abstract

Background
Plasma amyloid-beta (Aβ), neurofilament light chain (NfL), and progranulin (PGRN) have been related to multiple neurodegenerative conditions that might affect physical performance. The aim of this study was to explore the relationship between these plasma neurodegenerative markers and physical performance among community-dwelling older adults.

Methods
Five hundred and seven older adults (aged 76 ± 5 years) previously recruited in the Multidomain Alzheimer’s Preventive Trial, and had received blood and physical performance tests, were included in this study. Plasma Aβ (Aβ 42/Aβ 40 ratio), NfL, and PGRN levels were measured. Physical performance was assessed by handgrip strength and the Short Physical Performance Battery (combining gait speed, chair stands, and balance tests). Physical performance measured at the same time point and after the blood tests were used. Mixed-effect linear models were performed with age, sex, allocation to Multidomain Alzheimer’s Preventive Trial group, body mass index, and Mini-Mental State Examination score as covariates.

Results
The mean values of Aβ 42/Aβ 40 ratio, NfL, and PGRN were 0.11, 84.06 pg/mL, and 45.43 ng/mL, respectively. At the cross-sectional level, higher plasma NfL was associated with a lower Short Physical Performance Battery score (β = −0.004, 95% CI [−0.007, −0.001]). At the longitudinal level, higher PGRN levels were associated with decreasing handgrip strength over time (β = −0.02, 95% CI [−0.04, −0.007]). All the other associations were statistically nonsignificant.

Conclusion
Our findings suggest the possibility of using plasma NfL and PGRN as markers of physical performance in older adults.
Nursing Home Residents With Dementia: Association Between Place of Death and Patient Safety Culture
Authors: Orth Jessica , Li Yue , Simning Adam , Zimmerman Sheryl , Temkin-Greener Helena 
Published: November 2020

Abstract

Background and Objectives
Nursing homes (NHs) care for 70% of Americans dying with dementia. Many consider deaths in NHs rather than hospitals as preferable for most of these residents. NH characteristics such as staff teamwork, communication, and other components of patient safety culture (PSC), together with state minimum NH nurse staffing requirements, may influence location of death. We examined associations between these variables and place of death (NH/hospital) among residents with dementia.

Research Design and Methods
Cross-sectional study of 11,957 long-stay NH residents with dementia, age 65+, who died in NHs or hospitals shortly following discharge from one of 800 U.S. NHs in 2017. Multivariable logistic regression systematically estimated effects of PSC on odds of in-hospital death among residents with dementia, controlling for resident, NH, county, and state characteristics. Logistic regressions also determined moderating effects of state minimum NH nurse staffing requirements on relationships between key PSC domains and location of death.

Results
Residents with dementia in NHs with higher PSC scores in communication openness had lower odds of in-hospital death. This effect was stronger in NHs located in states with higher minimum NH nurse staffing requirements.

Discussion and Implications
Promoting communication openness in NHs across nursing disciplines may help avoid unnecessary hospitalization at the end of life, and merits particular attention as NHs address nursing staff mix while adhering to state staffing requirements. Future research to better understand unintended consequences of staffing requirements is needed to improve end-of-life care in NHs.
Patient-specific 3-dimensional lung modelling: next-generation imaging helps guide precise surgical resection
Authors: Baig Mirza Zain , Muslim Zaid , Weber Joanna F , Bhora Faiz Y 
Published: November 2020

Abstract
Recent strides have allowed the consolidation of routine imaging modalities with highly accurate reconstruction software to aid the operating surgeon generate patient-specific three-dimensional models. In this preliminary report, we describe our initial experience using a patient-specific reconstruction software to guide surgical resection for 2 patients with non-small-cell lung cancer. Digital imaging and communications in medicine data from patient chest CT scans was configured into IQQA BodyImaging Lung software to generate highly accurate maps of airways, vessels and segments as well as estimates of lung volumes. Models generated aided us in planning appropriate lung cancer resection procedures.
Sofosbuvir and daclatasvir for the treatment of COVID-19 outpatients: a double-blind, randomized controlled trial
Authors: Roozbeh Fatemeh , Saeedi Majid , Alizadeh-Navaei Reza , Hedayatizadeh-Omran Akbar , Merat Shahin , Wentzel Hannah , Levi Jacob , Hill Andrew , Shamshirian Amir 
Published: November 2020

Abstract

Introduction
Effective treatments are urgently needed to tackle the novel coronavirus disease 2019 (COVID-19). This trial aims to evaluate sofosbuvir and daclatasvir versus standard care for outpatients with mild COVID-19 infection.

Methods
This was a randomized controlled clinical trial in outpatients with mild COVID-19. Patients were randomized into a treatment arm receiving sofosbuvir/daclatasvir plus hydroxychloroquine or a control arm receiving hydroxychloroquine alone. The primary endpoint of the trial was symptom alleviation after 7 days of follow-up. The secondary endpoint of the trial was hospital admission. Fatigue, dyspnoea and loss of appetite were investigated after 1 month of follow-up. This study is registered with the IRCT.ir under registration number IRCT20200403046926N1.

Results
Between 8 April 2020 and 19 May 2020, 55 patients were recruited and allocated to either the sofosbuvir/daclatasvir treatment arm (n = 27) or the control arm (n = 28). Baseline characteristics were similar across treatment arms. There was no significant difference in symptoms at Day 7. One patient was admitted to hospital in the sofosbuvir/daclatasvir arm and four in the control arm, but the difference was not significant. After 1 month of follow-up, two patients reported fatigue in the sofosbuvir/daclatasvir arm and 16 in the control arm; P &lt; 0.001.

Conclusions
In this study, sofosbuvir/daclatasvir did not significantly alleviate symptoms after 7 days of treatment compared with control. Although fewer hospitalizations were observed in the sofosbuvir/daclatasvir arm, this was not statistically significant. Sofosbuvir/daclatasvir significantly reduced the number of patients with fatigue and dyspnoea after 1 month. Larger, well-designed trials are warranted.
Morphological Alterations of the Sarcotubular System in Permanent Myopathy of Hereditary Hypokalemic Periodic Paralysis with a Mutation in the CACNA1S Gene
Authors: Nagasaka Takamura , Hata Takanori , Shindo Kazumasa , Adachi Yoshiki , Takeuchi Megumi , Saito Kayoko , Takiyama Yoshihisa 
Published: November 2020

Abstract
We investigated the immunohistochemical localization of several proteins related to excitation-contraction coupling and ultrastructural alterations of the sarcotubular system in biopsied muscles from a father and a daughter in a family with permanent myopathy with hypokalemic periodic paralysis (PMPP) due to a mutation in calcium channel CACNA1S; p. R1239H hetero. Immunostaining for L-type calcium channels (LCaC) showed linear hyper-stained regions indicating proliferation of longitudinal t-tubules. The margin of vacuoles was positive for ryanodine receptor, LCaC, calsequestrin (CASQ) 1, CASQ 2, SR/ER Ca2+-ATPase (SERCA) 1, SERCA2, dysferlin, dystrophin, α-actinin, LC3, and LAMP 1. Electron microscopy indicated that the vacuoles mainly originated from the sarcoplasmic reticulum (SR). These findings indicate impairment of the muscle contraction system related to Ca2+ dynamics, remodeling of t-tubules and muscle fiber repair. We speculate that PMPP in patients with a CACNA1S mutation might start with abnormal SR function due to impaired LCaC. Subsequent induction of muscular contractile abnormalities and the vacuoles formed by fused SR in the repair process including autophagy might result in permanent myopathy. Our findings may facilitate prediction of the pathomechanisms of PMPP seen on morphological observation.
Results of definitive radiotherapy with concurrent chemotherapy for maxillary sinus carcinomas with neck lymph node metastasis
Authors: Abe Takanori , Saito Satoshi , Iino Misaki , Aoshika Tomomi , Ryuno Yasuhiro , Ohta Tomohiro , Igari Mitsunobu , Hirai Ryuta , Kumazaki Yu , Ebihara Yasuhiro , Nakahira Mitsuhiko , Sugasawa Masashi , Noda Shin-ei , Kato Shingo 
Published: November 2020

Abstract
The purpose of this study was to describe the results of definitive radiotherapy (RT) with concurrent chemotherapy for maxillary sinus carcinomas (MSCs) with neck lymph node metastasis to clarify its limitation. Local control (LC), progression-free survival (PFS) and overall survival (OS) rates were calculated using the Kaplan–Meier method and were compared between subgroups using the log rank test. Toxicity was classified using common terminology criteria of adverse events version 5.0. Eighteen patients with inoperable MSC with neck lymph node metastasis including 12 men and 6 women with a median age of 67 years were analyzed. The histologic diagnoses were as follows: 16 patients had squamous cell carcinomas and 2 had other histology. Four patients had stage T3 MSC, 6 had T4a and 8 had T4b. Among 18 patients, 7 received concurrent systemic chemotherapy and 11 received selective arterial chemo-infusion. The median follow-up period was 17 months. The 2-year LC, PFS and OS rates for the entire cohort were 34, 31 and 46%, respectively. No significant differences were observed for LC, PFS and OS rates between systemic chemotherapy and selective arterial chemo-infusion cohorts. Grade 3 or higher acute toxicity, including both non-hematological and hematological, was observed in nine patients (50%), while no grade 3 or higher late toxicity was observed. In conclusion, we described the results of definitive RT for MSCs with neck lymph node metastasis. Local recurrence of primary tumor was a frequent pattern of failure and it should be addressed in future study.
A delayed post-operative diaphragmatic hernia with hemothorax due to a strangulated stomach
Authors: Al-Saqqa Rama , Sabouni Rami , Jarad Lana , Abbas Nizar 
Published: November 2020

Abstract
Traumatic diaphragmatic hernias (TDHs) are uncommon, and they mostly occur following blunt or penetrating traumatic injury and rarely as a complication of Iatrogenic procedure. The management of TDHs is through surgical repair. In this article, we present the case of a diaphragmatic herniation presenting 1 year after thoracic surgery in a 16-year-old male. The patient presented with gastrointestinal obstruction symptoms and later developed a hypovolemic shock due to stomach bleeding. Immediate exploratory thoracotomy was performed, and the patient reached a full recovery afterward.
A multiscale assessment of Red-tailed Hawk reproductive success relative to urban density and habitat type
Authors: White Justin H , Brown Jessi L , Ormsby Zachary E 
Published: November 2020

AbstractDespite the unique threats to wildlife in urban areas, many raptors have established successfully reproducing urban populations. To identify variations in raptor breeding ecology within an urban area, we compared metrics of Red-tailed Hawk reproductive attempts to landscape characteristics in Reno and Sparks, NV, USA during the 2015 and 2016 breeding seasons. We used the Apparent Nesting Success and logistic exposure methods to measure nesting success of the Red-tailed Hawks. We used generalized linear models to relate nesting success and fledge rate to habitat type, productivity to hatch date (Julian day) and hatch date to urban density. Nesting success was 86% and 83% for the respective years. Nesting success increased in grassland-agricultural and shrub habitats and decreased in riparian habitat within the urban landscape. Productivity was 2.23 and 2.03 per nest for the breeding seasons. Fledge rates were 72% and 77%, respectively, and decreased in riparian areas. Nestlings hatched earlier with increased urban density and earliest in suburban areas, following a negative quadratic curve. Nesting success and productivity for this population were high relative to others in North America. Productivity increased in habitats where ground prey was more accessible. We suggest that suburban areas, if not frequently disturbed, provide sufficient resources to sustain Red-tailed Hawks over extended periods. As urban expansion continues in arid environments globally, we stress that researchers monitor reproductive output across the urban predator guild to elucidate patterns in population dynamics and adaptation.
Insights into the evo-devo of plant reproduction using next-generation sequencing approaches
Authors: Preston Jill C 
Published: November 2020

Abstract
The development of plant model organisms has traditionally been analyzed using resource-heavy, tailored applications that are not easily transferable to distantly related non-model taxa. Thus, our understanding of plant development has been limited to a subset of traits, and evolutionary studies conducted most effectively either across very wide [e.g. Arabidopsis thaliana and Oryza sativa (rice)] or narrow (i.e. population level) phylogenetic distances. As plant biologists seek to capitalize on natural diversity for crop improvement, enhance ecosystem functioning, and better understand plant responses to climate change, high-throughput and broadly applicable forms of existing molecular biology assays are becoming an invaluable resource. Next-generation sequencing (NGS) is increasingly becoming a powerful tool in evolutionary developmental biology (evo-devo) studies, particularly through its application to understanding trait evolution at different levels of gene regulation. Here, I review some of the most common and emerging NGS-based methods, using exemplar studies in reproductive plant evo-devo to illustrate their potential.
LeMMINGs – II. The e-MERLIN legacy survey of nearby galaxies. The deepest radio view of the Palomar sample on parsec scale
Authors: Baldi R D , Williams D R A , McHardy I M , Beswick R J , Brinks E , Dullo B T , Knapen J H , Argo M K , Aalto S , Alberdi A , Baan W A , Bendo G J , Corbel S , Fenech D M , Gallagher J S , Green D A , Kennicutt R C , Klöckner H-R , Körding E , Maccarone T J , Muxlow T W B , Mundell C G , Panessa F , Peck A B , Pérez-Torres M A , Romero-Cañizales C , Saikia P , Shankar F , Spencer R E , Stevens I R , Varenius E , Ward M J , Yates J , Uttley P 
Published: November 2020

ABSTRACT
We present the second data release of high-resolution (≤0.2 arcsec) 1.5-GHz radio images of 177 nearby galaxies from the Palomar sample, observed with the e-MERLIN array, as part of the Legacy e-MERLIN Multi-band Imaging of Nearby Galaxies Sample (LeMMINGs) survey. Together with the 103 targets of the first LeMMINGs data release, this represents a complete sample of 280 local active (LINER and Seyfert) and inactive galaxies (H ii galaxies and absorption line galaxies, ALG). This large program is the deepest radio survey of the local Universe, ≳1017.6 W Hz−1, regardless of the host and nuclear type: we detect radio emission ≳0.25 mJy beam−1 for 125/280 galaxies (44.6 per cent) with sizes of typically ≲100 pc. Of those 125, 106 targets show a core which coincides within 1.2 arcsec with the optical nucleus. Although we observed mostly cores, around one third of the detected galaxies features jetted morphologies. The detected radio core luminosities of the sample range between ∼1034 and 1040 erg s−1. LINERs and Seyferts are the most luminous sources, whereas H ii galaxies are the least. LINERs show FR I-like core-brightened radio structures while Seyferts reveal the highest fraction of symmetric morphologies. The majority of H ii galaxies have single radio core or complex extended structures, which probably conceal a nuclear starburst and/or a weak active nucleus (seven of them show clear jets). ALGs, which are typically found in evolved ellipticals, although the least numerous, exhibit on average the most luminous radio structures, similar to LINERs.
Model of heat diffusion in the outer crust of bursting neutron stars
Authors: Yakovlev D G , Kaminker A D , Potekhin A Y , Haensel P 
Published: November 2020

ABSTRACT
We study heat diffusion after an energy release in a deep spherical layer of the outer neutron star crust (107 ≲ ρ ≲ 4 × 1011 g cm−3). We demonstrate that this layer possesses specific heat-accumulating properties, absorbing heat and directing it mostly inside the star. It can absorb up to ∼1043–1044 erg due to its high heat capacity, until its temperature exceeds T ∼ 3 × 109 K and triggers a rapid neutrino cooling. A warm layer (T ∼ 108–3 × 109 K) can serve as a good heat reservoir, which is thermally decoupled from the inner crust and the stellar core for a few months. We present a toy model to explore the heat diffusion within the heat-accumulating layer, and we test this model using numerical simulations. We formulate some generic features of the heat propagation that can be useful, for instance, for the interpretation of superbursts in accreting neutron stars. We present a self-similar analysis of late afterglow after such superbursts, which can be helpful to estimate properties of bursting stars.
On the possibility of probing the flare productivity of an active region in the early stage of emergence
Authors: Kutsenko Alexander S , Abramenko Valentina I , Kutsenko Olga K 
Published: November 2020

ABSTRACT
Prediction of the future flare productivity of an active region (AR) when it is in the early-emergence stage is a longstanding problem. The aim of this study is to probe two parameters of the photospheric magnetic field, both derived during the emergence phase of an AR, and to compare them with the flare productivity of a well developed AR. The parameters are: (i) the index of the magnetic power spectrum (the slope of the spectrum) at the stage of emergence, and (ii) the flux emergence rate. Analysis of 243 emerging ARs showed that the magnetic power index increases from values typical of quiet-Sun regions to those typical of mature ARs within a day, while the emergence proceeds for several days; frequently, after the increase, the value of the power index oscillates around some mean value with the fluctuations being several times smaller than the growth of the power index during the emergence onset. For a subset of 34 flare-productive ARs we found no correlation between the power spectrum index at the stage of emergence and the flare index derived from the entire interval of the AR’s presence on the disc. At the same time, the flux emergence rate correlates well with the flare index (Pearson’s correlation coefficient is 0.74). We conclude that a high flux emergence rate is a necessary condition for an AR to produce strong flares in the future; thus the flux emergence rate can be used to probe the future flare productivity of an AR.