bluuebunny/crossref_metadata_2025_split huggingface dataset:
A loop-mediated isothermal amplification assay for Schistosoma mansoni detection in Biomphalaria spp. from schistosomiasis-endemic areas in Minas Gerais, Brazil
Authors: Mesquita Silvia Gonçalves , Neves Floria Gabriela dos Santos , Scholte Ronaldo Guilherme Carvalho , Carvalho Omar dos Santos , Fonseca Cristina Toscano , Caldeira Roberta Lima 
Published: August 2021

Abstract
Background
Schistosomiasis a neglected tropical disease endemic in Brazil. It is caused by the trematode Schistosoma mansoni, which is transmitted by snails of the genus Biomphalaria. Among measures used to control and eliminate schistosomiasis, accurate mapping and monitoring of snail breeding sites are recommended. Despite the limitations of parasitological methods, they are still used to identify infected snails. Loop-mediated isothermal amplification (LAMP) is a sensitive, rapid, and cost-effective diagnostic method for the identification of infected snails. In the work reported here, we aimed to validate the use of LAMP for the detection of S. mansoni in snails of the genus Biomphalaria.

Methods
Snails were collected in five municipalities of the Mucuri Valley and Jequitinhonha Valley regions in the state of Minas Gerais, Brazil. Snails were pooled according to collection site and then squeezed for the detection of S. mansoni and other trematode larvae. Pooled snails were subjected to pepsin digestion and DNA extraction. Molecular assays were performed for species-specific identification and characterization of the samples. A previously described LAMP assay was adapted, evaluated, and validated using laboratory and field samples.

Results
Using the parasitological method described here, S. mansoni cercariae were detected in snails from two collection sites, and cercariae of the family Spirorchiidae were found in snails from one site. The snails were identified by polymerase chain reaction (PCR)–restriction fragment length polymorphism (RFLP). Biomphalaria glabrata, the main snail host of S. mansoni in Brazil, was detected in 72.2% of the collection sites. Biomphalaria kuhniana, which is resistant to S. mansoni infection, was found in the remaining sites. Multiplex, low stringency (LS), and conventional PCR allowed the detection of positive snails in four additional sites. Trematodes belonging to the families Strigeidae and Echinostomatidae were detected by multiplex PCR in two sites. The LAMP assay was effective in detecting the presence of S. mansoni infection in laboratory (7 days post-infection) and field samples with no cross-reactivity for other trematodes. When compared to LS and conventional PCR, LAMP showed 100% specificity, 85.7% sensitivity, and a κ index of 0.88.

Conclusions
Our findings suggest that LAMP is a good alternative method for the detection and monitoring of transmission foci of S. mansoni, as it was three times as effective as the parasitological examination used here for the detection of infection, and is more directly applicable in the field than other molecular techniques.

Graphical abstract
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2
Authors: Patiño-Galindo Juan Ángel , Filip Ioan , Chowdhury Ratul , Maranas Costas D. , Sorger Peter K. , AlQuraishi Mohammed , Rabadan Raul 
Published: August 2021

Abstract
Background
The emergence of SARS-CoV-2 underscores the need to better understand the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. In the betacoronavirus genus, which also includes SARS-CoV and MERS-CoV, recombination frequently encompasses the receptor binding domain (RBD) of the Spike protein, which is responsible for viral binding to host cell receptors. In this work, we reconstruct the evolutionary events that have accompanied the emergence of SARS-CoV-2, with a special emphasis on the RBD and its adaptation for binding to its receptor, human ACE2.

Methods
By means of phylogenetic and recombination analyses, we found evidence of a recombination event in the RBD involving ancestral linages to both SARS-CoV and SARS-CoV-2. We then assessed the effect of this recombination at protein level by reconstructing the RBD of the closest ancestors to SARS-CoV-2, SARS-CoV, and other Sarbecoviruses, including the most recent common ancestor of the recombining clade. The resulting information was used to measure and compare, in silico, their ACE2-binding affinities using the physics-based trRosetta algorithm.

Results
We show that, through an ancestral recombination event, SARS-CoV and SARS-CoV-2 share an RBD sequence that includes two insertions (positions 432-436 and 460-472), as well as the variants 427N and 436Y. Both 427N and 436Y belong to a helix that interacts directly with the human ACE2 (hACE2) receptor. Reconstruction of ancestral states, combined with protein-binding affinity analyses, suggests that the recombination event involving ancestral strains of SARS-CoV and SARS-CoV-2 led to an increased affinity for hACE2 binding and that alleles 427N and 436Y significantly enhanced affinity as well.

Conclusions
We report an ancestral recombination event affecting the RBD of both SARS-CoV and SARS-CoV-2 that was associated with an increased binding affinity to hACE2. Structural modeling indicates that ancestors of SARS-CoV-2 may have acquired the ability to infect humans decades ago. The binding affinity with the human receptor would have been subsequently boosted in SARS-CoV and SARS-CoV-2 through further mutations in RBD.
Delayed functional therapy after acute lateral ankle sprain increases subjective ankle instability – the later, the worse: a retrospective analysis
Authors: Raeder Christian , Tennler Janina , Praetorius Arthur , Ohmann Tobias , Schoepp Christian 
Published: August 2021

Abstract
Background
The lateral ankle sprain (LAS) is one of the most common injuries in everyday and sports activities. Approximately 20–40 % of patients with LAS develop a chronic ankle instability (CAI). The underlying mechanisms for CAI have not yet been clearly clarified. An inadequate rehabilitation after LAS can be speculated, since the LAS is often handled as a minor injury demanding less treatment. Therefore, the aims of this retrospective study were to determine the CAI rate depending on age and sex and to identify possible determinants for developing CAI.

Methods
Between 2015 and 2018 we applied the diagnostic code “sprain of ankle” (ICD S93.4) to identify relevant cases from the database of the BG Klinikum Duisburg, Germany. Patients received a questionnaire containing the Tegner-Score, the Cumberland Ankle Instability Tool (CAIT) and the Foot and Ankle Disability Index. Additionally, there were questions about the modality and beginning of therapy following LAS and the number of recurrent sprains. There was a total of 647 completed datasets. These were divided into a CAI and non-CAI group according to a CAIT cut-off-score with CAI ≤ 24 and non-CAI > 24 points, representing one out of three criteria for having CAI based on international consensus.

Results
The overall CAI rate was 17.3 %. We identified a higher CAI rate in females and within the age segment of 41 to 55 years. A later start of therapy (> 4 weeks) after acute LAS significantly increases ankle instability in CAIT (p < .05). There was a significantly higher CAIT score in patients having no recurrent sprain compared to patients having 1–3 recurrent sprains or 4–5 recurrent sprains (p < .001).

Conclusions
Females over 41 years show a higher CAI rate which implies to perform specific prevention programs improving ankle function following acute LAS. A delayed start of therapy seems to be an important determinant associated with the development of CAI. Another contributing factor may be a frequent number of recurrent sprains that are also linked to greater levels of subjective ankle instability. Therefore, we would recommend an early start of functional therapy after acute LAS in the future to minimize the development of CAI.
MPDB 2.0: a large scale and integrated medicinal plant database of Bangladesh
Authors: Hussain Nazmul , Chanda Rony , Abir Ruhshan Ahmed , Mou Mohsina Akter , Hasan Md. Kamrul , Ashraf M. Arif 
Published: August 2021

Abstract
Objective
MPDB 2.0 is built to be the continuation of MPDB 1.0, to serve as a more comprehensive data repertoire for Bangladeshi medicinal plants, and to provide a user-friendly interface for researchers, health practitioners, drug developers, and students who wish to study the various medicinal & nutritive plants scattered around Bangladesh and the underlying phytochemicals contributing to their efficacy in Bangladeshi folk medicine.

Results
MPDB 2.0 database (https://www.medicinalplantbd.com/) comprises a collection of more than five hundred Bangladeshi medicinal plants, alongside a record of their corresponding scientific, family, and local names together with their utilized parts, information regarding ailments, active compounds, and PubMed ID of related publications. While medicinal plants are not limited to the borders of any country, Bangladesh and its Southeast Asian neighbors do boast a huge collection of potent medicinal plants with considerable folk-medicinal history compared to most other countries in the world. Development of MPDB 2.0 has been highly focused upon human diseases, albeit many of the plants indexed here can serve in developing biofuel (e.g.: Jatropha curcas used in biofuel) or bioremediation technologies (e.g.: Amaranthus cruentus helps to reduce cadmium level in soil) or nutritive diets (Terminalia chebula can be used in nutritive diets) or cosmetics (Aloe vera used in cosmetics), etc.
Acute kidney injury prevalence, progression and long-term outcomes in critically ill patients with COVID-19: a cohort study
Authors: Lumlertgul Nuttha , Pirondini Leah , Cooney Enya , Kok Waisun , Gregson John , Camporota Luigi , Lane Katie , Leach Richard , Ostermann Marlies 
Published: August 2021

AbstractBackgroundThere are limited data on acute kidney injury (AKI) progression and long-term outcomes in critically ill patients with coronavirus disease-19 (COVID-19). We aimed to describe the prevalence and risk factors for development of AKI, its subsequent clinical course and AKI progression, as well as renal recovery or dialysis dependence and survival in this group of patients.MethodsThis was a retrospective observational study in an expanded tertiary care intensive care unit in London, United Kingdom. Critically ill patients admitted to ICU between 1st March 2020 and 31st July 2020 with confirmed SARS-COV2 infection were included. Analysis of baseline characteristics, organ support, COVID-19 associated therapies and their association with mortality and outcomes at 90 days was performed.ResultsOf 313 patients (70% male, mean age 54.5 ± 13.9 years), 240 (76.7%) developed AKI within 14 days after ICU admission: 63 (20.1%) stage 1, 41 (13.1%) stage 2, 136 (43.5%) stage 3. 113 (36.1%) patients presented with AKI on ICU admission. Progression to AKI stage 2/3 occurred in 36%. Risk factors for AKI progression were mechanical ventilation [HR (hazard ratio) 4.11; 95% confidence interval (CI) 1.61–10.49] and positive fluid balance [HR 1.21 (95% CI 1.11–1.31)], while steroid therapy was associated with a reduction in AKI progression (HR 0.73 [95% CI 0.55–0.97]). Kidney replacement therapy (KRT) was initiated in 31.9%. AKI patients had a higher 90-day mortality than non-AKI patients (34% vs. 14%;p < 0.001). Dialysis dependence was 5% at hospital discharge and 4% at 90 days. Renal recovery was identified in 81.6% of survivors at discharge and in 90.9% at 90 days. At 3 months, 16% of all AKI survivors had chronic kidney disease (CKD); among those without renal recovery, the CKD incidence was 44%.ConclusionsDuring the first COVID-19 wave, AKI was highly prevalent among severely ill COVID-19 patients with a third progressing to severe AKI requiring KRT. The risk of developing CKD was high. This study identifies factors modifying AKI progression, including a potentially protective effect of steroid therapy. Recognition of risk factors and monitoring of renal function post-discharge might help guide future practice and follow-up management strategies.Trial registrationNCT04445259
Downlink multi-user algorithms for millimeter-wave wideband linear arrays on PD-NOMA-based squint steering beams
Authors: Pan Xiaoliang , Yang Luxi 
Published: August 2021

AbstractThis article investigates using a phased linear antenna array instead of the planar array to circumvent the problem that two frequency squint steering main beams cannot cover any two beam directions simultaneously. First, we approximate the donut-shaped main beam of the linear array by means of multiple pencil-shaped main beams of a virtual planar array for matching the steering main beam of the linear array with the multi-path sparse scattering channel model mathematically and give a method for calculating the number of antenna elements of the virtual array. Second, we cope with possible inter-user interference on a single squint main beam of the linear array in some scenarios by means of the power-domain non-orthogonal multiple access (PD-NOMA) technique, making it possible to support communication with two users on a single squint main beam at the base station (BS) side. The feasible domain of PD-NOMA is given when a single antenna is used for both the BS and the user end, assuming a two-user successive interference cancellation (SIC) decoding power ratio limit. Third, three algorithms are given for serving multi-user at the BS via squint beams of the linear array. Finally, numerical results show that the second proposed algorithm supporting PD-NOMA pairing within a single donut-shaped squint main beam significantly increases the number of simultaneous users served within a single cellular system.
Well posedness of a nonlinear mixed problem for a parabolic equation with integral condition
Authors: Djerad Abdelkader , Memou Ameur , Hameida Ali 
Published: August 2021

AbstractThe aim of this work is to prove the well posedness of some posed linear and nonlinear mixed problems with integral conditions. First, an a priori estimate is established for the associated linear problem and the density of the operator range generated by the considered problem is proved by using the functional analysis method. Subsequently, by applying an iterative process based on the obtained results for the linear problem, the existence, uniqueness of the weak solution of the nonlinear problems is established.
Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome
Authors: Roth-Schulze Alexandra J. , Penno Megan A. S. , Ngui Katrina M. , Oakey Helena , Bandala-Sanchez Esther , Smith Alannah D. , Allnutt Theo R. , Thomson Rebecca L. , Vuillermin Peter J. , Craig Maria E. , Rawlinson William D. , Davis Elizabeth A. , Harris Mark , Soldatos Georgia , Colman Peter G. , Wentworth John M. , Haynes Aveni , Barry Simon C. , Sinnott Richard O. , Morahan Grant , Bediaga Naiara G. , Smyth Gordon K. , Papenfuss Anthony T. , Couper Jennifer J. , Harrison Leonard C. ,   on behalf of the ENDIA Study Group
Published: August 2021

Abstract
Background
The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D.

Results
Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage.

Conclusions
Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means.
A generalized Fourier transform by means of change of variables within multilinear approximation
Authors: Chevreuil Mathilde , Slama Myriam 
Published: August 2021

AbstractThe paper deals with approximations of periodic functions that play a significant role in harmonic analysis. The approach revisits the trigonometric polynomials, seen as combinations of functions, and proposes to extend the class of models of the combined functions to a wider class of functions. The key here is to use structured functions, that have low complexity, with suitable functional representation and adapted parametrizations for the approximation. Such representation enables to approximate multivariate functions with few eventually random samples. The new parametrization is determined automatically with a greedy procedure, and a low rank format is used for the approximation associated with each new parametrization. A supervised learning algorithm is used for the approximation of a function of multiple random variables in tree-based tensor format, here the particular Tensor Train format. Adaptive strategies using statistical error estimates are proposed for the selection of the underlying tensor bases and the ranks for the Tensor-Train format. The method is applied for the estimation of the wall pressure for a flow over a cylinder for a range of low to medium Reynolds numbers for which we observe two flow regimes: a laminar flow with periodic vortex shedding and a laminar boundary layer with a turbulent wake (sub-critic regime). The automatic re-parametrization enables here to take into account the specific periodic feature of the pressure.
Monocyte-to-lymphocyte ratio is associated with 28-day mortality in patients with acute respiratory distress syndrome: a retrospective study
Authors: Yang Lijuan , Gao Chang , Li Fengyuan , Yang Ling , Chen Jiahao , Guo Shiqi , He Ying , Guo Qiang 
Published: August 2021

Abstract
Background
Systemic inflammation relates to the initiation and progression of acute respiratory distress syndrome (ARDS). Neutrophil-to-lymphocyte ratio (NLR) and red blood cell distribution width (RDW)/albumin ratio have been reported to be predictive prognostic biomarkers in ARDS patients. However, the role of monocyte-to-lymphocyte ratio (MLR) as a prognostic inflammatory biomarker in a variety of diseases is rarely mentioned in ARDS. In this study, we explored the relationship between MLR and disease severity in ARDS patients and compared it with other indicators associated with 28-day mortality in patients with ARDS.

Methods
We retrospectively included 268 patients who fulfilled the Berlin definition of ARDS and were admitted to a single institute from 2016 to 2020. Clinical characteristics and experimental test data were collected from medical records within 24 h after the ARDS diagnosis. MLR, NLR, and RDW/albumin ratio levels were calculated. The primary clinical outcome was 28-day mortality. Logistic regression analysis was used to illustrate the relationship between indicators and 28-day mortality. Receiver operating characteristic (ROC) curve was used to evaluate the area under the curve (AUC), and propensity score matching (PSM) was employed to validate our findings.

Results
The median MLR values were higher for non-survivors than for survivors before and after matching (P<0.001, P=0.001, respectively). MLR values were significantly associated with 28-day mortality (OR 2.956; 95% CI 1.873–4.665; P<0.001). MLR and NLR indicators were combined for predictive efficacy analysis, and its AUC reached 0.750. There was a significant increase in 28-day mortality depending on the increasing MLR level: low MLR group 38 (20.4%), high MLR group 47 (57.3%) (P<0.001).

Conclusions
Higher MLR values were associated with 28-day mortality in patients with ARDS. Further investigation is required to verify this relationship with prospectively collected data.
Am I getting through? Surveying students on what messages they recall from the first day of STEM classes
Authors: Meaders Clara L. , Senn Lillian G. , Couch Brian A. , Lane A. Kelly , Stains Marilyne , Stetzer MacKenzie R. , Vinson Erin , Smith Michelle K. 
Published: August 2021

Abstract
Background
The first day of class helps students learn about what to expect from their instructors and courses. Messaging used by instructors, which varies in content and approach on the first day, shapes classroom social dynamics and can affect subsequent learning in a course. Prior work established the non-content Instructor Talk Framework to describe the language that instructors use to create learning environments, but little is known about the extent to which students detect those messages. In this study, we paired first day classroom observation data with results from student surveys to measure how readily students in introductory STEM courses detect non-content Instructor Talk.

Results
To learn more about the instructor and student first day experiences, we studied 11 introductory STEM courses at two different institutions. The classroom observation data were used to characterize course structure and use of non-content Instructor Talk. The data revealed that all instructors spent time discussing their instructional practices, building instructor/student relationships, and sharing strategies for success with their students. After class, we surveyed students about the messages their instructors shared during the first day of class and determined that the majority of students from within each course detected messaging that occurred at a higher frequency. For lower frequency messaging, we identified nuances in what students detected that may help instructors as they plan their first day of class.

Conclusions
For instructors who dedicate the first day of class to establishing positive learning environments, these findings provide support that students are detecting the messages. Additionally, this study highlights the importance of instructors prioritizing the messages they deem most important and giving them adequate attention to more effectively reach students. Setting a positive classroom environment on the first day may lead to long-term impacts on student motivation and course retention. These outcomes are relevant for all students, but in particular for students in introductory STEM courses which are often critical prerequisites for being in a major.