bluuebunny/crossref_metadata_2025_split huggingface dataset:
The clinical efficacy and safety of dapagliflozin in patients with diabetic nephropathy
Authors: Huang Ying , Lu Wen , Lu Hongyun 
Published: March 2022

Abstract
Objective
To investigate the clinical efficacy and safety of dapagliflozin in the treatment of diabetic nephropathy (DN).

Methods
A total of 120 DN patients admitted to our hospital from June 2017 to March 2020 were divided into control and experimental groups, with 60 cases in each group. The control group received valsartan, and the experimental group received dapagliflozin for 3 months. Body mass index (BMI), hemoglobin A1c (HbA1c), serum creatinine (sCr), uric acid (UA), urine microalbumin (uMA), urine creatinine (uCr), and bilateral kidney function were compared before and after treatment, and adverse reactions in both groups were observed. Serum interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels were also evaluated.

Results
After treatment, except for BMI in the control group, all indexes in both groups were significantly improved. The BMI, HbA1c, sCr, UA, and uMA/uCr ratios of the experimental group were lower than those of the control group. Serum albumin (sAlb) levels were increased in both groups, and the experimental group showed a significant difference compared with the control group. Estimated glomerular filtration rate (eGFR) levels were increased in both groups, and the experimental group was higher than the control group, with no significant differences. Serum IL-6 and TNF-α levels in both groups were lower, and the experimental group was significantly lower than the control group. No serious adverse reactions were observed in either group.

Conclusion
The efficacy of dapagliflozin was demonstrated by its ability to improve diabetes, prevent nephropathy exacerbation, and reduce symptomatic reactions. The low rate of adverse reactions makes dapagliflozin a very safe medication.
Structure-based design and construction of a synthetic phage display nanobody library
Authors: Moreno Ernesto , Valdés-Tresanco Mario S. , Molina-Zapata Andrea , Sánchez-Ramos Oliberto 
Published: March 2022

AbstractObjectiveTo design and construct a new synthetic nanobody library using a structure-based approach that seeks to maintain high protein stability and increase the number of functional variants within the combinatorial space of mutations.ResultsSynthetic nanobody (Nb) libraries are emerging as an attractive alternative to animal immunization for the selection of stable, high affinity Nbs. Two key features define a synthetic Nb library: framework selection and CDR design. We selected the universal VHH framework from the cAbBCII10 Nb. CDR1 and CDR2 were designed with the same fixed length as in cAbBCII10, while for CDR3 we chose a 14-long loop, which creates a convex binding site topology. Based on the analysis of the cAbBCII10 crystal structure, we carefully selected the positions to be randomized and tailored the codon usage at each position, keeping at particular places amino acids that guarantee stability, favoring properties like polarity at solvent-exposed positions and avoiding destabilizing amino acids. Gene synthesis and library construction were carried out by GenScript, using our own phagemid vector. The constructed library has an estimated size of 1.75 × 108. NGS showed that the amino acid diversity and frequency at each randomized position are the expected from the codon usage.
Metabolic impact of a nutrition education program for the promotion of fruit and vegetable consumption with people with severe mental disorders (DIETMENT)
Authors: Foguet-Boreu Quintí , Vilamala-Orra Mireia , Vaqué-Crusellas Cristina , Roura-Poch Pere , Assens Tauste Montse , Bori Vila Judit , Santos-López Jose Manuel , del Río Sáez Ruben 
Published: March 2022

AbstractObjectivesThe aim of this study is to determine the metabolic impact of a nutrition education program on metabolic parameters and the presence of metabolic syndrome (MetS).ResultsSeventy-four patients were included (mean age, 48.7 years [Standard deviation, SD: 10.8], 55.4% men). The diagnoses of SMD were 37.8% schizophrenia and related disorders; 29.7% bipolar disorder; 25.7% depressive disorder; 4.1% personality disorders; and 2.7% obsessive compulsive disorders. Thirty-seven individuals were distributed in both the intervention group (IG) and the control group (CG). In the IG the presence of MetS was 56.3% and in the CG 46.7%, with no statistically significant difference (p = 0.309). At the end of the study, glomerular filtrate decreased in the IG, body mass index and abdominal perimeter increased in both groups, and there were no changes in metabolic parameters between the groups. Between the baseline and the end of the study, there was no increase in the number of patients diagnosed with MetS (14 at both points); and in the CG the increase was from 8 to 12 (p = 0.005). An intervention based on fruit and vegetable intake could prevent progression to MetS in individuals with SMD, decreasing the likelihood of cardiovascular disease.Trial registrationThe trial was retrospectively registered on International Standard Randomised Controlled Trial Number (ISRCTN) Register on 11 March 2022 (ISRCTN12024347)
The effect of lesion filling on brain network analysis in multiple sclerosis using structural magnetic resonance imaging
Authors: van der Weijden Chris W. J. , Pitombeira Milena S. , Haveman Yudith R. A. , Sanchez-Catasus Carlos A. , Campanholo Kenia R. , Kolinger Guilherme D. , Rimkus Carolina M. , Buchpiguel Carlos A. , Dierckx Rudi A. J. O. , Renken Remco J. , Meilof Jan F. , de Vries Erik F. J. , de Paula Faria Daniele 
Published: March 2022

Abstract
Background
Graph theoretical network analysis with structural magnetic resonance imaging (MRI) of multiple sclerosis (MS) patients can be used to assess subtle changes in brain networks. However, the presence of multiple focal brain lesions might impair the accuracy of automatic tissue segmentation methods, and hamper the performance of graph theoretical network analysis. Applying “lesion filling” by substituting the voxel intensities of a lesion with the voxel intensities of nearby voxels, thus creating an image devoid of lesions, might improve segmentation and graph theoretical network analysis. This study aims to determine if brain networks are different between MS subtypes and healthy controls (HC) and if the assessment of these differences is affected by lesion filling.

Methods
The study included 49 MS patients and 19 HC that underwent a T1w, and T2w-FLAIR MRI scan. Graph theoretical network analysis was performed from grey matter fractions extracted from the original T1w-images and T1w-images after lesion filling.

Results
Artefacts in lesion-filled T1w images correlated positively with total lesion volume (r = 0.84, p < 0.001) and had a major impact on grey matter segmentation accuracy. Differences in sensitivity for network alterations were observed between original T1w data and after application of lesion filling: graph theoretical network analysis obtained from lesion-filled T1w images produced more differences in network organization in MS patients.

Conclusion
Lesion filling might reduce variability across subjects resulting in an increased detection rate of network alterations in MS, but also induces significant artefacts, and therefore should be applied cautiously especially in individuals with higher lesions loads.
Comparative performance of fully-automated and semi-automated artificial intelligence methods for the detection of clinically significant prostate cancer on MRI: a systematic review
Authors: Sushentsev Nikita , Moreira Da Silva Nadia , Yeung Michael , Barrett Tristan , Sala Evis , Roberts Michael , Rundo Leonardo 
Published: March 2022

Abstract
Objectives
We systematically reviewed the current literature evaluating the ability of fully-automated deep learning (DL) and semi-automated traditional machine learning (TML) MRI-based artificial intelligence (AI) methods to differentiate clinically significant prostate cancer (csPCa) from indolent PCa (iPCa) and benign conditions.

Methods
We performed a computerised bibliographic search of studies indexed in MEDLINE/PubMed, arXiv, medRxiv, and bioRxiv between 1 January 2016 and 31 July 2021. Two reviewers performed the title/abstract and full-text screening. The remaining papers were screened by four reviewers using the Checklist for Artificial Intelligence in Medical Imaging (CLAIM) for DL studies and Radiomics Quality Score (RQS) for TML studies. Papers that fulfilled the pre-defined screening requirements underwent full CLAIM/RQS evaluation alongside the risk of bias assessment using QUADAS-2, both conducted by the same four reviewers. Standard measures of discrimination were extracted for the developed predictive models.

Results
17/28 papers (five DL and twelve TML) passed the quality screening and were subject to a full CLAIM/RQS/QUADAS-2 assessment, which revealed a substantial study heterogeneity that precluded us from performing quantitative analysis as part of this review. The mean RQS of TML papers was 11/36, and a total of five papers had a high risk of bias. AUCs of DL and TML papers with low risk of bias ranged between 0.80–0.89 and 0.75–0.88, respectively.

Conclusion
We observed comparable performance of the two classes of AI methods and identified a number of common methodological limitations and biases that future studies will need to address to ensure the generalisability of the developed models.
Recolonization by Indigenous broadleaved species of a conifer plantation (Cupressus spp.) in Northern Iran after 25 years
Authors: Jafarzade Masoud , Ravanbakhsh Hooman , Moshki Alireza , Mollashahi Maryam 
Published: March 2022

Abstract
Key message
A vegetation analysis revealed the extent of recolonization by native vegetation of a 25-year-old Cupressus spp. plantation in northern Iran. A young indigenous Quercus-Carpinus community replaced the conifers in the low-slope areas with deeper, heavier, and more fertile soils.

Context
Reforestation of degraded or clear-cut-harvested lands can modify site conditions, facilitating succession and reestablishing native forests. It is critical to investigate the plantation in terms of vegetation, natural regeneration, and environmental variables to better understand ecological restoration.

Aims
This study examines the recolonization of a Cypress plantation by native vegetation in the deforested Hyrcanian broadleaf forests and determines which edaphic, topographic, and structural variables are correlated to the degree of reconstitution.

Methods
A systematic random sampling method was used to establish 55 plots in a 25-year-old Cupressus plantation, followed by plot classification using TWINSPAN and environment-vegetation analysis using CCA. The classification groups were compared using an analysis of variance. Tested variables included floristic composition, stand structure, regeneration, topography, and soil parameters.

Results
Four vegetation groups were identified based on an analysis of floristic composition. The first group demonstrated the least degree of native forest reconstitution, as planted conifers (Cupressus spp.) were established alongside pioneer broadleaf shrubs, enhancing Zelkova carpinifolia (Pall.) K.Koch regeneration. While most conifers disappeared in the third group, Carpinus betulus L., Zelkova carpinifolia, and Quercus castaneifolia C.A. Mey became dominant. The most influential environmental factors in reestablishing indigenous communities were a low-slope, heavier soil with a higher organic carbon and potassium content.

Conclusion
On low-slope lands with fertile soils, the Hyrcanian native broadleaf forest can recolonize the coniferous plantation; however, on steep lands with poor sandy soils, planted Cupressus trees as well as relatively xerophytic shrubs in the understory may establish.
Heuristic approaches for the car sequencing problems with block batches
Authors: Yu Yingjie , Lu Xiaochun , Zhao Tao , Cheng Minjiao , Liu Lin , Wei Wenchao 
Published: March 2022

AbstractMotivated by the practical supply chain management of the automobile industry, we study the car sequencing problem (CSP) that minimizes the conflicts occur when sequentially manufacturing cars on an assembly line. The CSP is a well-established problem, subject to the paint batching constraints to decrease the energy consumption for color changeovers and production rate constraints in the assembly shop to ensure a smooth usage of car options. However, the existing solution algorithms to this problem do not take into account the block batches, which desires a consecutive production batch of cars requiring a certain option. This requirement often occurs when specialized labor time window is short in the customized car production scenario, and renders additional complexities to the traditional car sequencing problem. In this paper, we present a novel model to deal with these constraints and simultaneously generate the sequencing and replenishment decisions. Besides, we develop two math-heuristic algorithms to solve the proposed large-scale CSP. The presented heuristics are on the basis of relax-and-fix procedures, fix-and-optimize procedures and adaptive variable neighborhood search. To solve the large-sized instances (commercial solvers, i.e., Cplex, cannot obtain a feasible result within 1 h), we design and implement a reinforced parameter tuning mechanism to dynamically select the parameter values, so as to speed up the search process. The proposed models and heuristics are tested on representative instances generated from the benchmark in the literature (CSPLib), as well as large-sized instances generated from real-world cases. We report on extensive computational experiments and provide basic managerial insights into the planning process.
A framework of evidence-based decision-making in health system management: a best-fit framework synthesis
Authors: Shafaghat Tahereh , Bastani Peivand , Nasab Mohammad Hasan Imani , Bahrami Mohammad Amin , Montazer Mahsa Roozrokh Arshadi , Zarchi Mohammad Kazem Rahimi , Edirippulige Sisira 
Published: March 2022

Abstract
Background
Scientific evidence is the basis for improving public health; decision-making without sufficient attention to evidence may lead to unpleasant consequences. Despite efforts to create comprehensive guidelines and models for evidence-based decision-making (EBDM), there isn`t any to make the best decisions concerning scarce resources and unlimited needs. The present study aimed to develop a comprehensive applied framework for EBDM.

Methods
This was a Best-Fit Framework (BFF) synthesis conducted in 2020. A comprehensive systematic review was done via six main databases including PUBMED, Scopus, Web of Science, Science Direct, EMBASE, and ProQuest using related keywords. After the evidence quality appraisal, data were extracted and analyzed via thematic analysis. Results of the thematic analysis and the concepts generated by the research team were then synthesized to achieve the best-fit framework applying Carroll et al. (2013) approach.

Results
Four thousand six hundred thirteen studies were retrieved, and due to the full-text screening of the studies, 17 final articles were selected for extracting the components and steps of EBDM in Health System Management (HSM). After collecting, synthesizing, and categorizing key information, the framework of EBDM in HSM was developed in the form of four general scopes. These comprised inquiring, inspecting, implementing, and integrating, which included 10 main steps and 47 sub-steps.

Conclusions
The present framework provided a comprehensive guideline that can be well adapted for implementing EBDM in health systems and related organizations especially in underdeveloped and developing countries where there is usually a lag in updating and applying evidence in their decision-making process. In addition, this framework by providing a complete, well-detailed, and the sequential process can be tested in the organizational decision-making process by developed countries to improve their EBDM cycle.
Principles and framework for assessing the risk of bias for studies included in comparative quantitative environmental systematic reviews
Authors: Frampton Geoff , Whaley Paul , Bennett Micah , Bilotta Gary , Dorne Jean-Lou C. M. , Eales Jacqualyn , James Katy , Kohl Christian , Land Magnus , Livoreil Barbara , Makowski David , Muchiri Evans , Petrokofsky Gillian , Randall Nicola , Schofield Kate 
Published: March 2022

AbstractThe internal validity of conclusions about effectiveness or impact in systematic reviews, and of decisions based on them, depends on risk of bias assessments being conducted appropriately. However, a random sample of 50 recently-published articles claiming to be quantitative environmental systematic reviews found 64% did not include any risk of bias assessment, whilst nearly all that did omitted key sources of bias. Other limitations included lack of transparency, conflation of quality constructs, and incomplete application of risk of bias assessments to the data synthesis. This paper addresses deficiencies in risk of bias assessments by highlighting core principles that are required for risk of bias assessments to be fit-for-purpose, and presenting a framework based on these principles to guide review teams on conducting risk of bias assessments appropriately and consistently. The core principles require that risk of bias assessments be Focused, Extensive, Applied and Transparent (FEAT). These principles support risk of bias assessments, appraisal of risk of bias tools, and the development of new tools. The framework follows a Plan-Conduct-Apply-Report approach covering all stages of risk of bias assessment. The scope of this paper is comparative quantitative environmental systematic reviews which address PICO or PECO-type questions including, but not limited to, topic areas such as environmental management, conservation, ecosystem restoration, and analyses of environmental interventions, exposures, impacts and risks.
Rapid and efficient colorimetric sensing of clindamycin and Fe3+ using controllable phyto-synthesized silver/silver chloride nanoparticles by Syzygium cumini fruit extract
Authors: Ebrahimi Atefeh , Samari Fayezeh , Eftekhar Ebrahim , Yousefinejad Saeed 
Published: March 2022

Abstract
The first evidence of a green, single-step, and additive-free process for the fabrication of silver/silver chloride nanoparticles (Ag/AgCl NPs) by fruit extract of Syzygium cumini (S. cumini) without the usage of any stabilizer and halide source was provided. The formation of nanoparticles was optimized to control the shape, size, and stability via various pHs of the reaction mixture, the quantity of fruit extract, temperature, concentrations of silver ion, and reaction time. The optimal conditions were determined: pH = 7.0, the quantity of the leaf extract = 3.0 mL, silver ion concentration = 1.0 mM, temperature = 60 °C, and incubation time = 40 min. As an application in colorimetric sensing, the ability of the prepared Ag/AgCl NPs to sense clindamycin and Fe3+ ion in an aqueous medium was investigated. The SPR band and color of the solution of Ag/AgCl NPs undergo dramatic changes in exposure to clindamycin with new SPR peaks appearing at 500 nm, accompanied by a color change from yellow to pink due to the aggregation of NPs. Under the optimized pH of 3.0, this sensor was shown a linear dynamic range from 10.0 to 100.0 µM with a LOD of 1.2 µM and good linear relationships (R2 = 0.99) for clindamycin. On the other hand, the quenching of the SPR peak at 412 nm was used to monitor the Fe3+ ions with wide linear ranges of 10.0–350.0 µM under the optimized pH (pH = 9) with a LOD of 5.6 µM. In addition, the proposed sensor displayed applicability in the real sample containing clindamycin (in capsules and injection ampoules) and Fe3+ ions (in water samples) detection.

Graphical Abstract
Mendel’s controlled pollination experiments in Mirabilis jalapa confirmed his discovery of the gamete theory of inheritance in Pisum
Authors: Zhang Hui , Zhao Xiaoxi , Zhao Fan , Han Jianshan , Sun Kun 
Published: March 2022

AbstractThe historian studies revealed during Mendel’s later research period when mainly focusing on the constant hybrid in Hieracium, he had to be intervened to conduct the controlled pollination experiments in Mirabilis jalapa. Two letters to Nageli recorded the experimental aim was to disprove Darwin’s opinion regarding three pollen grains required for one fertilization (note: that could completely destroy his previous discovery of segregation inheritance in variable hybrid in Pisum, for it was expressed in a mathematical equation). The experimental results of single pollen grain pollination confirmed the referenced view of one pollen cell uniting one egg cell in plant fertilization; the further pedigree introduction of the single and of the designed two pollen grain experiment succeeded in exemplifying that one hereditary factor carried by one gamete (pollen cell or egg cell) can independently transmit a trait to offspring. Here we coined the observation as the Gamete Theory of Inheritance. Remarkably, in contrast with the bulked pollination experiment, in this system, Mendel could easily manipulate a hereditary factor by merely taking a gamete as a carrier. Then, Mendel’s work in M. jalapa together with the previous Pisum study was able to jointly suppport his second lecture content that regarded “gamete formation, fertilization, and seed development” and also regarded hereditary factors in the processes. All in all, the 1866 paper was published during a rapid burst of interest in hybrid species likely induced by Darwin, and Mendel’s attempts at accommodation of the two incompatible inheritances of segregation in variable hybrids versus of nonsegregation in constant hybrids might be responsible for some historical controversies when understanding his discovery of inheritance.
A cost-effective three-dimensional marine controlled-source electromagnetic survey: Exploring seafloor massive sulfides
Authors: Ishizu Keiichi , Siripunvaraporn Weerachai , Goto Tada-nori , Koike Katsuaki , Kasaya Takafumi , Iwamoto Hisanori 
Published: March 2022

A 3D marine controlled-source electromagnetic (CSEM) survey for mapping hydrocarbons uses dozens of ocean-bottom electric (OBE) receivers deployed in a grid pattern and several transmitter towlines. This study considers seafloor massive sulfides (SMS) exploration, and the horizontal survey scale of SMS is a few kilometers, which is small compared with hydrocarbon surveys of tens of kilometers. If we apply a 3D CSEM survey using a receiver deployment on grids to map SMS, high survey costs will be incurred despite the small survey size. We have developed a cost-effective 3D marine CSEM survey that uses fewer receivers than the survey with a receiver deployment on grids to reduce survey costs for SMS. This CSEM survey uses a line of OBE receivers in the center of the survey area and several transmitter towlines. Numerical tests demonstrate that our survey (seven OBE receivers) using 80% fewer receivers than the survey with a receiver deployment on grids (35 OBE receivers) is able to accurately map SMS, obtaining a performance similar to that of the receiver deployment on grids. Then, we explore SMS in the Ieyama hydrothermal area off Okinawa, southwest Japan, using our 3D CSEM survey with a line of six OBE receivers and three transmitter towlines. The resulting 3D resistivity distribution from the observed data highlights three potential SMS zones consisting of 0.2 ohm-m low resistivity embedded into 1 ohm-m sediment.