bluuebunny/crossref_metadata_2025_split huggingface dataset:
GENPPI: standalone software for creating protein interaction networks from genomes
Authors: Ferreira William , Lanes Gabriel , Azevedo Vasco , Santos Anderson 
Published: January 2021

AbstractMotivationBacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships that are capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.ResultsWe developed GENPPI software for theab initioprediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genusCorynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the speciesCorynebacterium pseudotuberculosisand created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 minutes on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships among species and were obtained in average nucleotide identity (ANI) analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user’s choice regarding which set of genomes he or she is going to study.AvailabilityThe source code in the Common Lisp language, binary files for different operating systems, and GENPPI software tutorials are available at {{github.com/santosardr/genppi}}.Contactsantosardr@ufu.brSupplementary informationSupplementary data are available atBioinformaticsonline.
A generalization of t-SNE and UMAP to single-cell multimodal omics
Authors: Do Van Hoan , Canzar Stefan 
Published: January 2021

AbstractEmerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP. We introduce j-SNE and j-UMAP as their natural generalizations to the joint visualization of multimodal omics data. Our approach automatically learns the relative contribution of each modality to a concise representation of cellular identity that promotes discriminative features but suppresses noise. On eight datasets, j-SNE and j-UMAP produce unified embeddings that better agree with known cell types and that harmonize RNA and protein velocity landscapes. j-SNE and j-UMAP are available in the JVis Python package.
Global transcriptome analysis ofStenotrophomonas maltophiliain response to growth at human body temperature
Authors: Patil Prashant P. , Kumar Sanjeet , Kaur Amandeep , Midha Samriti , Bansal Kanika , Patil Prabhu B. 
Published: January 2021

AbstractStenotrophomonas maltophilia(Smal) is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 ◻) is higher than environmental niches (22-30 ◻). Interestingly,S. rhizophilaa phylogenetic neighbour of Smal within genusStenotrophomonasis unable to grow at 37 ◻. Thus, it is crucial to understand how Smal is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis ofS. maltophiliagrown at 28 ◻ and 37 ◻ as temperature representative for environmental niches and human body respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene expression levels at 28 ◻ and 37 ◻, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 Type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 ◻. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed byS. maltophiliaduring adaptation towards the human body.Impact statementStenotrophomonas maltophilia(Smal) is a WHO listed multidrug resistant nosocomial pathogen. Interestingly,S. maltophiliaspecies can grow both at 28 ◻ and 37 ◻ unlike its closest taxonomic relative, i.e.,S. rhizophilaand also majority species belonging this genus. Hence this ability to grow at 37 ◻, i.e., human body temperature might have played key role in the unique success and emergence of this species as opportunistic human pathogen. Using transcriptome sequencing, we have identified set of genes which are differentially regulated at 37 ◻ and investigated their evolutionary history. This study has revealed regulation of genes involved in motility, metabolism, energy, replication, transcription, aerotaxis and a type IV secretion system might have a role in successful adaption to a distinct lifestyle. The findings will be helpful in further systematic studies on understanding and management of an emerging human pathogen such as Smal.
Cultural information needs of long-settled immigrants, their descendants and family members: use of collective and personal information sources about the home country
Authors: Krtalic Maja 
Published: January 2021

PurposeThis paper presents findings from a study that explored why and how long-settled immigrants, their descendants and family members seek and use information about their country of origin and how they manage personal information about their cultural heritage legacy.Design/methodology/approach15 semi-structured interviews were conducted with participants from the Croatian community in New Zealand.FindingsThe main findings reveal two categories of information needs related to a home country: internally motivated and externally motivated. Information is accessed through a network of family and friends, cultural societies and embassies. These information sources are perceived as reliable and trustworthy, and able to offer an interpretation of information along with access to information. The findings highlight the value of personal collections as information sources and the impact of personal information management practices on preserving and sharing information about one's cultural heritage.Originality/valueThis article contributes to the discussion about information needs and practices of immigrant communities by offering arguments that focus on (1) long-settled immigrants, their descendants and family members, and (2) seeking information about home country culture and heritage, and (3) the role of personal collections and personal information management in maintaining personal cultural heritage. The results of this study may be of use to libraries, archives and museums in designing and offering their services to expatriates of their country and immigrants in their country, and to the wider information management sector developing services in personal information management.
Labour supply responses to financial wealth shocks: evidence from Italy
Authors: Bottazzi Renata , Trucchi Serena , Wakefield Matthew 
Published: January 2021

AbstractWe look at how strongly shocks to wealth affect labour supply, using Italian data. We use asset price shocks to provide a measure of wealth changes that is exogenous to the household's saving and labour supply. Results point to significant effects of wealth on hours of work, whether agents leave their jobs and labour earnings. The magnitude of these effects can be substantial – for example, for individuals who suffered larger wealth losses during the financial crisis. Responses are similar for men and women on average, but older working‐age individuals have relatively strong responses that drive the population results. Short‐run effects are somewhat persistent.
An Evaluation of Remotely Sensed and In Situ Data Sufficiency for SGMA‐Scale Groundwater Studies in the Central Valley, California
Authors: Kim Kyra H. , Liu Zhen , Rodell Matthew , Beaudoing Hiroko , Massoud Elias , Kitchens James , Dudek Marissa , Saylor Patrick , Corcoran Forrest , Reager John T. 
Published: January 2021

AbstractCalifornia’s Central Valley aquifer is a critical freshwater resource for the state, providing drinking water to 6.5 million residents and irrigation water for more than half of the nation’s produce. Increasing demands have led to a steady decline of aquifer water levels, leading to irreversible compaction and land subsidence. The Sustainable Groundwater Management Act of California (SGMA), instituted in 2014, requires high‐priority regions to establish sustainability plans by 2020–2022 that mitigate groundwater depletion and land subsidence. Many regions within the Central Valley lack groundwater monitoring wells or continuous well data, rendering in situ monitoring challenging. When combined with other data, National Aeronautics and Space Administration’s Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow‐On missions provide valuable information about groundwater storage changes at a subbasin scale. Interferometric Synthetic Aperture Radar measurements can map land subsidence, and Global Positioning System can be used to estimate crustal uplift. Yet, all of these measurements have differences in resolution, coverage, discretization, and record length. Here we assess the various datasets that are potentially useful for Central Valley subbasin groundwater monitoring and provide an analysis of gaps and other issues in regard to their suitability for SGMA‐related analysis. Finally, we offer the next steps and recommendations on data treatment and integration.
Comparative analysis of the Memorial Sloan Kettering Bowel Function Instrument and the Low Anterior Resection Syndrome Questionnaire for assessment of bowel dysfunction in rectal cancer patients after low anterior resection
Authors: Quezada‐Diaz Felipe F. , Elfeki Hossam , Emmertsen Katrine J. , Pappou Emmanouil P. , Jimenez‐Rodriguez Rosa , Patil Sujata , Laurberg Søren , Garcia‐Aguilar Julio 
Published: January 2021

AbstractAimNeoadjuvant therapy and total mesorectal excision (TME) for rectal cancer are associated with bowel dysfunction symptoms known as low anterior resection syndrome (LARS). Our study compared the only two validated instruments—the LARS Questionnaire (LARS‐Q) and the Memorial Sloan Kettering Bowel Function Instrument (MSK‐BFI)—in rectal cancer patients undergoing sphincter‐preserving TME.MethodsOne hundred and ninety patients undergoing sphincter‐preserving TME for Stage I–III rectal cancer completed the MSK‐BFI and LARS‐Q simultaneously at a median time of 12 (range 1–43) months after restoration of bowel continuity. Associations between the MSK‐BFI total/subscale scores and the LARS‐Q score were investigated using Spearman rank correlation (r s). Discriminant validity for the two questionnaires was assessed, and the questionnaires were compared with the European Quality of Life Instrument.ResultsMajor LARS was identified in 62% of patients. The median MSK‐BFI scores for no LARS, minor LARS and major LARS were 76.5, 70 and 57, respectively. We found a strong association between MSK‐BFI and LARS‐Q (r s −0.79). The urgency/soilage subscale (r s −0.7) and the frequency subscale (rs −0.68) of MSK‐BFI strongly correlated with LARS‐Q. Low correlation was observed between the MSK‐BFI diet subscale and LARS‐Q (r s −0.39). On multivariate analysis, both questionnaires showed worse bowel function in patients with distal tumours. A low to moderate correlation with the European Quality of Life Instrument was observed for both questionnaires.ConclusionsThe MSK‐BFI and LARS‐Q showed good correlation and similar discriminant validity. As the LARS‐Q is easier to complete, it may be considered the preferred tool to screen for bowel dysfunction.
In children and young people with type 1 diabetes using Pump therapy, an additional 40% of the insulin dose for a high‐fat, high‐protein breakfast improves postprandial glycaemic excursions: A cross‐over trial
Authors: Smith Tenele A. , Smart Carmel E. , Fuery Michelle E. J. , Howley Peter P. , Knight Brigid A. , Harris Mark , King Bruce R. 
Published: January 2021

ABSTRACTAimTo determine the insulin requirement for a high‐fat, high‐protein breakfast to optimise postprandial glycaemic excursions in children and young people with type 1 diabetes using insulin pumps.MethodsIn all, 27 participants aged 10–23 years, BMI <95th percentile (2–18 years) or BMI <30 kg/m2 (19–25 years) and HbA1c ≤64 mmol/mol (≤8.0%) consumed a high‐fat, high‐protein breakfast (carbohydrate: 30 g, fat: 40 g and protein: 50 g) for 4 days. In this cross‐over trial, insulin was administered, based on the insulin‐to‐carbohydrate ratio (ICR) of 100% (control), 120%, 140% and 160%, in an order defined by a randomisation sequence and delivered in a combination bolus, 60% ¼ hr pre‐meal and 40% over 3 hr. Postprandial sensor glucose was assessed for 6 hr.ResultsComparing 100% ICR, 140% ICR and 160% ICR resulted in significantly lower 6‐hr areas under the glucose curves: mean (95%CI) (822 mmol/L.min [605,1039] and 567 [350,784] vs 1249 [1042,1457], p ≤ 0.001) and peak glucose excursions (4.0 mmol/L [3.0,4.9] and 2.7 [1.7,3.6] vs 6.0 [5.0,6.9],p < 0.001). Rates of hypoglycaemia for 100%‐160% ICR were 7.7%, 7.7%, 12% and 19% respectively (p ≥ 0.139). With increasing insulin dose, a step‐wise reduction in mean glucose excursion was observed from 1 to 6 hr (p = 0.008).ConclusionsIncrementally increasing the insulin dose for a high‐fat, high‐protein breakfast resulted in a predictable, dose‐dependent reduction in postprandial glycaemia: 140% ICR improved postprandial glycaemic excursions without a statistically significant increase in hypoglycaemia. These findings support a safe, practical method for insulin adjustment for high‐fat, high‐protein meals that can be readily implemented in practice to improve postprandial glycaemia.
Green Flags and headache: A concept study using the Delphi method
Authors: Pohl Heiko , Do Thien Phu , García‐Azorín David , Hansen Jakob Møller , Kristoffersen Espen Saxhaug , Nelson Sarah E. , Obermann Mark , Sandor Peter S. , Schankin Christoph J. , Schytz Henrik Winther , Sinclair Alexandra , Schoonman Guus G. , Gantenbein Andreas R. 
Published: January 2021

AbstractObjectiveThe aim of this study was to collect and rate Green Flags, that is, symptoms or pieces of information indicating that a patient is more likely to suffer from a primary than from a secondary headache.BackgroundWhen assessing headaches, a central question to be answered is whether the pain is primary or secondary to another disorder. To maximize the likelihood of a correct diagnosis, relevant signs and symptoms must be sought, identified, and weighed against each other.MethodsThe project was designed as a Delphi study. In the first round, an expert panel proposed green flags that were rated anonymously in two subsequent rounds. Proposals with an average rating of 4.0 and higher on a scale from 0 to 5 reached consensus.ResultsFive Green Flags reached consensus: (i) “The current headache has already been present during childhood”; (ii) “The headache occurs in temporal relationship with the menstrual cycle”; (iii) “The patient has headache‐free days“; (iv) “Close family members have the same headache phenotype”; and (v) “Headache occurred or stopped more than one week ago.”ConclusionsWe propose five Green Flags for primary headache disorders. None being a pathognomonic sign, we recommend searching for both Green Flags and Red Flags. If both are present, a secondary headache should be suspected. Overall, the application of the Green Flag concept in clinical practice is likely to increase diagnostic accuracy and improve diagnostic resource allocation. Prospective studies in clinical populations should be conducted to validate these Green Flags.
Formononetin ameliorates muscle atrophy by regulating myostatin‐mediated PI3K/Akt/FoxO3a pathway and satellite cell function in chronic kidney disease
Authors: Liu Lingyu , Hu Rong , You Haiyan , Li Jingjing , Liu Yangyang , Li Qiang , Wu Xiaohui , Huang Jiawen , Cai Xiangsheng , Wang Mingqing , Wei Lianbo 
Published: January 2021

AbstractMuscle atrophy is a common complication in chronic kidney disease (CKD). Inflammation and myostatin play important roles in CKD muscle atrophy. Formononetin (FMN), which is a major bioactive isoflavone compound in Astragalus membranaceus, exerts anti‐inflammatory effects and the promotion of myogenic differentiation. Our study is based on myostatin to explore the effects and mechanisms of FMN in relation to CKD muscle atrophy. In this study, CKD rats and tumour necrosis factor α (TNF‐α)‐induced C2C12 myotubes were used for in vivo and in vitro models of muscle atrophy. The results showed that FMN significantly improved the renal function, nutritional status and inflammatory markers in CKD rats. Values for bodyweight, weight of tibialis anterior and gastrocnemius muscles, and cross‐sectional area (CSA) of skeletal muscles were significantly larger in the FMN treatment rats. Furthermore, FMN significantly suppressed the expressions of MuRF‐1, MAFbx and myostatin in the muscles of CKD rats and the TNF‐α‐induced C2C12 myotubes. Importantly, FMN significantly increased the phosphorylation of PI3K, Akt, and FoxO3a and the expressions of the myogenic proliferation and differentiation markers, myogenic differentiation factor D (MyoD) and myogenin in muscles of CKD rats and the C2C12 myotubes. Similar results were observed in TNF‐α‐induced C2C12 myotubes transfected with myostatin‐small interfering RNA (si‐myostatin). Notably, myostatin overexpression plasmid (myostatin OE) abolished the effect of FMN on the phosphorylation of the PI3K/Akt/FoxO3a pathway and the expressions of MyoD and myogenin. Our findings suggest that FMN ameliorates muscle atrophy related to myostatin‐mediated PI3K/Akt/FoxO3a pathway and satellite cell function.
Significance of immediate dentin sealing and flowable resin coating reinforcement for unfilled/lightly filled adhesive systems
Authors: de Carvalho Marco Aurélio , Lazari‐Carvalho Priscilla Cardoso , Polonial Isabella Fonseca , de Souza João Batista , Magne Pascal 
Published: January 2021

AbstractBackgroundImmediate dentin sealing implies applying an adhesive system to dentin directly after tooth preparation, before impression. The technique is universal (inlays, onlays, veneers, crowns) and well documented clinically and experimentally. Different types of dentin bonding agents (DBAs) are available on the market. Major differences lie in the thickness of the hybrid layer and overlaying adhesive resin (filled vs. unfilled/lightly filled adhesives).ObjectiveThe objective of this work is to provide precise clinical instructions and present new experimental data about the bond strength of five DBAs (Optibond FL, Scotchbond MP, Single Bond Plus, Clearfil SE Bond, and Scotchbond Universal) used conventionally (dentin sealed at the time of restoration delivery) or with immediate dentin sealing, as well as with an additional flowable resin coating.MethodsSeventy‐five human molars were selected, restored/tested according the microtensile bond strength method. Fifteen groups (n=5) were obtained from the combination of the five DBAs and three application modes: delayed dentin sealing, immediate dentin sealing and immediate dentin sealing with flowable resin coating.ResultsIt appears that immediate dentin sealing was confirmed to significantly improve the bond strength of all tested adhesives. The use of a flowable resin coating reinforcement after immediate dentin sealing increased the microtensile bond strength of all unfilled/lightly filled adhesives (from 233% of increase for ScotchBond MP, up to 560% for Clearfil SE Bond) and maintained the performance of the 3‐step golden standard adhesive. Optibond FL used with (52.51 MPa) or without (54.75 MPa) additional flowable resin coating and Clearfil SE Bond (45.64 MPa) used with flowable resin coating provided the best results.Clinical SignificanceThe original immediate dentin sealing (IDS) technique implies the use of a filled DBA. With unfilled/lightly filled adhesives, it is suggested to reinforce IDS with an additional flowable resin coating. This seems especially paramount to the performance of simplified adhesive systems to protect the thin bonding interface from oxygen inhibition and preserve IDS layer during predelivery cleaning of the preparation. The clinical reinforcement of unfilled/lightly filled IDS with flowable resin composite is encouraged for more predictable bonding.
Hematopoietic cell transplant for reversal of liver fibrosis in a pediatric patient with erythropoietic protoporphyria
Authors: Hashmi Saman K. , Harstead Elaine , Sachdev Mansi , Black Dennis D. , Clark Ian , Ortanca Ibrahim , Triplett Brandon M. , Talleur Aimee C. 
Published: January 2021

AbstractBackgroundEPP is a rare disorder of heme biosynthesis in which patients present with disabling photosensitivity. A subset of patients develop severe liver disease with progressive liver failure necessitating an OLT. A HCT can potentially cure EPP by replacing the native bone marrow, which is the primary site of heme synthesis. However, due to concerns for inherent risks of treatment‐related toxicities, the use of HCT has been reserved for patients undergoing an OLT to avoid disease recurrence in the hepatic graft. Data for HCT in EPP are lacking, particularly in the pediatric population.Case (Methods/Results)We present the case of a 12‐year‐old patient with EPP photosensitivity and cirrhosis, whom we successfully treated with pre‐emptive allogeneic HCT, significantly improving the patient's quality of life. We used a matched‐unrelated donor bone marrow–derived graft. Our patient achieved full donor peripheral blood chimerism and has not had any evidence of GVHD. In addition to resolution of photosensitivity, our patient had reversal of liver fibrosis which we feel was largely due to intervention at an early stage of compensated cirrhosis.ConclusionOur case highlights the successful application of a known RIC regimen to this rare disorder that was well tolerated with sustained donor engraftment. It also emphasizes the importance of timing for HCT in patients with EPP and liver fibrosis. HCT should be considered early in pediatric patients with EPP‐hepatopathy to prevent progression to liver failure and need for OLT with lifelong immunosuppression.