bluuebunny/crossref_metadata_2025_split huggingface dataset:
The limitations of external measurements for aging small mammals: the cautionary example of the Lesser Treeshrew (Scandentia: Tupaiidae: Tupaia minor Günther, 1876)
Authors: Woodman Neal , Miller-Murthy Ananth , Olson Link E , Sargis Eric J 
Published: May 2021

Abstract
Age is a basic demographic characteristic vital to studies of mammalian social organization, population dynamics, and behavior. To eliminate potentially confounding ontogenetic variation, morphological comparisons among populations of mammals typically are limited to mature individuals (i.e., those assumed to have ceased most somatic growth). In our morphometric studies of treeshrews (Scandentia), adult individuals are defined by the presence of fully erupted permanent dentition, a common criterion in specimen-based mammalogy. In a number of cases, however, we have had poorly sampled populations of interest in which there were potentially useful specimens that could not be included in samples because they lacked associated skulls. Such specimens typically are associated with external body and weight measurements recorded by the original collectors, and we sought to determine whether these data could be used successfully as a proxy for age or at least to establish maturity. We analyzed four traditional external dimensions (head-and-body length, tail length, hind foot length, and ear length) and weight associated with 103 specimens from two allopatric populations of the Lesser Treeshrew (Tupaia minor Günther, 1876) from Peninsular Malaysia and from Borneo, which we treated as separate samples (populations). Individuals were assigned to one of eight age categories based on dental eruption stage, and measurements were compared among groups. In general, mean sizes of infants and subadults were smaller than those of adults, but the majority of subadults fell within the range of variation of adults. The large overlap among infants, subadults, and adults in external measurements and weight indicates that such measures are poor proxies for age in this species, probably for treeshrews in general, and possibly for other small mammals. This has significant implications for any investigation wherein relative age of individuals in a given population is an important consideration.
Niche partitioning in small mammals: interspecific and biome-level analyses using stable isotopes
Authors: Bubadué Jamile , Cáceres Nilton , Melo Geruza , Sponchiado Jonas , Battistella Thaís , Newton Jason , Meloro Carlo 
Published: May 2021

Abstract
Small mammal assemblages from South America provide a unique opportunity to measure coexistence and niche partitioning between marsupials and placentals. We tested how these two major clades partition environmental resources by comparing stable isotopic ratios of similar sized Didelphidae and Sigmodontinae in four Brazilian biomes: Pampas grassland, Pantanal wetland, Cerrado woodland savanna, and Atlantic Forest. Generally, didelphid isotopic niche follows a scaling law, because we found an association between δ15N enrichment and body mass. Sigmodontines that primarily partition the environment via forest strata showed a greater intake of C4 or/and crassulacean acid metabolism (CAM) plants than didelphids, as reflected by their wider trophic niche. Values of δ13C were highest in savannas and grasslands (Cerrado and Pampas biomes), and values of δ15N were highest in the Atlantic Forest (in sigmodontines) and Pampas (in didelphids). While assessing patterns between the two major Brazilian biomes (Atlantic Forest and Cerrado), we found evidence of a broader trophic niche for both clades in the Cerrado. In the Atlantic Forest, niche occupation by Didelphidae was completely enclosed within the Sigmodontinae trophic niche. Both clades showed less overlap in the Cerrado, a less productive environment. Our results highlight the importance of a comparative framework and the use of stable isotopes for testing ecological questions related to how small mammalian communities partition their niche.
Long-term clinical outcomes of patients receiving proton beam therapy for caudate lobe hepatocellular carcinoma
Authors: Iizumi Takashi , Okumura Toshiyuki , Sekino Yuta , Takahashi Hiroaki , Tsai Yu-Lun , Takizawa Daichi , Ishida Toshiki , Hiroshima Yuichi , Nakamura Masatoshi , Shimizu Shosei , Saito Takashi , Numajiri Haruko , Mizumoto Masashi , Nakai Kei , Sakurai Hideyuki 
Published: May 2021

Abstract
Hepatocellular carcinoma (HCC) located in the caudate lobe (caudate HCC) is rare; however, patients with this type of tumour have poorer prognoses than those with HCC in other segments. Despite many published reports on the clinical usefulness of proton beam therapy (PBT) for HCC, data on the clinical outcomes of patients undergoing PBT for caudate HCC remain scarce. Therefore, the present study aimed to investigate the outcomes of this group of patients. Thirty patients with caudate HCC who underwent definitive PBT between February 2002 and February 2014 were retrospectively analysed. The total irradiation doses ranged from 55 to 77 (median 72.6) Gy relative biological dose. The median follow-up period was 37.5 (range, 3.0–152.0) months. The overall survival (OS) rates at one, three and five years were 86.6%, 62.8% and 46.1%, respectively. According to univariate and multivariate analyses, Child-Pugh A (P &lt; 0.01), having a single tumour (P = 0.02) and a low serum alpha-fetoprotein level (AFP; P &lt; 0.01) were significant factors predicting longer survival. The local control (LC) rates at one, three and five years were 100%, 85.9% and 85.9%, respectively, while the corresponding progression-free survival (PFS) rates were 65%, 27.5% and 22%, respectively. No grade 3 or worse adverse events were observed. PBT is effective and safe for the treatment of caudate HCC, and should therefore be considered a feasible option for intervention in patients with this disease.
Extrinsic compression of the right external iliac artery secondary to iliac vein stenting
Authors: Subramaniam Syva Imayan , Fung Adrian T , Taylor David C 
Published: May 2021

Abstract
Symptomatic extrinsic compression of the external iliac artery (EIA) is a rare complication of surgical intervention. Previous cases of EIA compression have presented in the postoperative period after orthopedic surgery or vascular stenting. We report a case of right EIA compression postvenous stenting causing acute limb ischemia.
Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome
Authors: Whelan Fiona J , Hall Rebecca J , McInerney James O 
Published: May 2021

AbstractA pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome’s accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas species for statistically significant coincident (i.e., co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other—but are not vertically inherited—are more likely to share functional categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into sets of genes that function together within a given strain. Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.
Translational accuracy of a tethered ribosome
Authors: Fabret Celine , Namy Olivier 
Published: May 2021

Abstract
Ribosomes are evolutionary conserved ribonucleoprotein complexes that function as two separate subunits in all kingdoms. During translation initiation, the two subunits assemble to form the mature ribosome, which is responsible for translating the messenger RNA. When the ribosome reaches a stop codon, release factors promote translation termination and peptide release, and recycling factors then dissociate the two subunits, ready for use in a new round of translation. A tethered ribosome, called Ribo-T, in which the two subunits are covalently linked to form a single entity, was recently described in Escherichia coli. A hybrid ribosomal RNA (rRNA) consisting of both the small and large subunit rRNA sequences was engineered. The ribosome with inseparable subunits generated in this way was shown to be functional and to sustain cell growth. Here, we investigated the translational properties of Ribo-T. We analyzed its behavior during amino acid misincorporation, −1 or +1 frameshifting, stop codon readthrough, and internal translation initiation. Our data indicate that covalent attachment of the two subunits modifies the properties of the ribosome, altering its ability to initiate and terminate translation correctly.
A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition
Authors: St-Pierre Patrick , Shaw Euan , Jacques Samuel , Dalgarno Paul A , Perez-Gonzalez Cibran , Picard-Jean Frédéric , Penedo J Carlos , Lafontaine Daniel A 
Published: May 2021

Abstract
Riboswitches are RNA sequences that regulate gene expression by undergoing structural changes upon the specific binding of cellular metabolites. Crystal structures of purine-sensing riboswitches have revealed an intricate network of interactions surrounding the ligand in the bound complex. The mechanistic details about how the aptamer folding pathway is involved in the formation of the metabolite binding site have been previously shown to be highly important for the riboswitch regulatory activity. Here, a combination of single-molecule FRET and SHAPE assays have been used to characterize the folding pathway of the adenine riboswitch from Vibrio vulnificus. Experimental evidences suggest a folding process characterized by the presence of a structural intermediate involved in ligand recognition. This intermediate state acts as an open conformation to ensure ligand accessibility to the aptamer and folds into a structure nearly identical to the ligand-bound complex through a series of structural changes. This study demonstrates that the add riboswitch relies on the folding of a structural intermediate that pre-organizes the aptamer global structure and the ligand binding site to allow efficient metabolite sensing and riboswitch genetic regulation.
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information
Authors: Yao Shuwei , You Ronghui , Wang Shaojun , Xiong Yi , Huang Xiaodi , Zhu Shanfeng 
Published: May 2021

AbstractWith the explosive growth of protein sequences, large-scale automated protein function prediction (AFP) is becoming challenging. A protein is usually associated with dozens of gene ontology (GO) terms. Therefore, AFP is regarded as a problem of large-scale multi-label classification. Under the learning to rank (LTR) framework, our previous NetGO tool integrated massive networks and multi-type information about protein sequences to achieve good performance by dealing with all possible GO terms (&gt;44 000). In this work, we propose the updated version as NetGO 2.0, which further improves the performance of large-scale AFP. NetGO 2.0 also incorporates literature information by logistic regression and deep sequence information by recurrent neural network (RNN) into the framework. We generate datasets following the critical assessment of functional annotation (CAFA) protocol. Experiment results show that NetGO 2.0 outperformed NetGO significantly in biological process ontology (BPO) and cellular component ontology (CCO). In particular, NetGO 2.0 achieved a 12.6% improvement over NetGO in terms of area under precision-recall curve (AUPR) in BPO and around 2.6% in terms of $\mathbf {F_{max}}$ in CCO. These results demonstrate the benefits of incorporating text and deep sequence information for the functional annotation of BPO and CCO. The NetGO 2.0 web server is freely available at http://issubmission.sjtu.edu.cn/ng2/.
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers
Authors: Zeng Shuai , Mao Ziting , Ren Yijie , Wang Duolin , Xu Dong , Joshi Trupti 
Published: May 2021

Abstract
G2PDeep is an open-access web server, which provides a deep-learning framework for quantitative phenotype prediction and discovery of genomics markers. It uses zygosity or single nucleotide polymorphism (SNP) information from plants and animals as the input to predict quantitative phenotype of interest and genomic markers associated with phenotype. It provides a one-stop-shop platform for researchers to create deep-learning models through an interactive web interface and train these models with uploaded data, using high-performance computing resources plugged at the backend. G2PDeep also provides a series of informative interfaces to monitor the training process and compare the performance among the trained models. The trained models can then be deployed automatically. The quantitative phenotype and genomic markers are predicted using a user-selected trained model and the results are visualized. Our state-of-the-art model has been benchmarked and demonstrated competitive performance in quantitative phenotype predictions by other researchers. In addition, the server integrates the soybean nested association mapping (SoyNAM) dataset with five phenotypes, including grain yield, height, moisture, oil, and protein. A publicly available dataset for seed protein and oil content has also been integrated into the server. The G2PDeep server is publicly available at http://g2pdeep.org. The Python-based deep-learning model is available at https://github.com/shuaizengMU/G2PDeep_model.
Thunor: visualization and analysis of high-throughput dose–response datasets
Authors: Lubbock Alexander L R , Harris Leonard A , Quaranta Vito , Tyson Darren R , Lopez Carlos F 
Published: May 2021

Abstract
High-throughput cell proliferation assays to quantify drug-response are becoming increasingly common and powerful with the emergence of improved automation and multi-time point analysis methods. However, pipelines for analysis of these datasets that provide reproducible, efficient, and interactive visualization and interpretation are sorely lacking. To address this need, we introduce Thunor, an open-source software platform to manage, analyze, and visualize large, dose-dependent cell proliferation datasets. Thunor supports both end-point and time-based proliferation assays as input. It provides a simple, user-friendly interface with interactive plots and publication-quality images of cell proliferation time courses, dose–response curves, and derived dose–response metrics, e.g. IC50, including across datasets or grouped by tags. Tags are categorical labels for cell lines and drugs, used for aggregation, visualization and statistical analysis, e.g. cell line mutation or drug class/target pathway. A graphical plate map tool is included to facilitate plate annotation with cell lines, drugs and concentrations upon data upload. Datasets can be shared with other users via point-and-click access control. We demonstrate the utility of Thunor to examine and gain insight from two large drug response datasets: a large, publicly available cell viability database and an in-house, high-throughput proliferation rate dataset. Thunor is available from www.thunor.net.
Relevance of gastrointestinal manifestations in a large Spanish cohort of patients with systemic lupus erythematosus: what do we know?
Authors: Tejera Segura Beatriz , Altabás González Irene , Rúa-Figueroa Iñigo , Pérez Veiga Natalia , Del Campo Pérez Victor , Olivé-Marqués Alejandro , Galindo María , Calvo Jaime , Ovalles-Bonilla Juan Gabriel , Fernández-Nebro Antonio , Menor-Almagro Raúl , Tomero Eva , del Val del Amo Natividad , Uriarte Isacelaya Esther , Martínez-Taboada Víctor Manuel , Andreu Jose L , Boteanu Alina , Narváez Javier , Movasat Atusa , Montilla Carlos , Senabre Gallego Jose Miguel , Hernández-Cruz Blanca , Andrés Mariano , Salgado Eva , Freire Mercedes , Machín García Sergio , Moriano Clara , Expósito Lorena , Pérez Velásquez Clara , Velloso-Feijoo M L , Cacheda Ana Paula , Lozano-Rivas Nuria , Bonilla Gema , Arévalo Marta , Jiménez Inmaculada , Quevedo-Vila Víctor , Manero-Ruiz Francisco J , García de la Peña Lefebvre Paloma , Vázquez-Rodríguez Tomás Ramón , Ibañez-Rua Jesús , Cobo-Ibañez Tatiana , Pego-Reigosa Jose María 
Published: May 2021

Abstract

Objective
SLE can affect any part of the gastrointestinal (GI) tract. GI symptoms are reported to occur in &gt;50% of SLE patients. To describe the GI manifestations of SLE in the RELESSER (Registry of SLE Patients of the Spanish Society of Rheumatology) cohort and to determine whether these are associated with a more severe disease, damage accrual and a worse prognosis.

Methods
We conducted a nationwide, retrospective, multicentre, cross-sectional cohort study of 3658 SLE patients who fulfil ≥4 ACR-97 criteria. Data on demographics, disease characteristics, activity (SLEDAI-2K or BILAG), damage (SLICC/ACR/DI) and therapies were collected. Demographic and clinical characteristics were compared between lupus patients with and without GI damage to establish whether GI damage is associated with a more severe disease.

Results
From 3654 lupus patients, 3.7% developed GI damage. Patients in this group (group 1) were older, they had longer disease duration, and were more likely to have vasculitis, renal disease and serositis than patients without GI damage (group 2). Hospitalizations and mortality were significantly higher in group 1. Patients in group 1 had higher modified SDI (SLICC Damage Index). The presence of oral ulcers reduced the risk of developing damage in 33% of patients.

Conclusion
Having GI damage is associated with a worse prognosis. Patients on a high dose of glucocorticoids are at higher risk of developing GI damage which reinforces the strategy of minimizing glucocorticoids. Oral ulcers appear to decrease the risk of GI damage.
Cerebral mansoni schistosomiasis: a systematic review of 33 cases published from 1989 to 2019
Authors: Bruscky Igor Silvestre , Bruscky Dayanne Mota Veloso , de Melo Fabio Lopes , Medeiros Zulma Maria , Correia Carolina da Cunha 
Published: May 2021

Abstract

Background
We investigated the epidemiology, clinical presentation and outcomes of individuals affected by cerebral schistosomiasis.

Methods
This systematic review was planned in accordance with current guidelines for performing comprehensive systematic reviews and meta-analysis, including the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline.

Results
Most of patients presented with seizures (48.5%), which is a non-specific symptom despite its high prevalence. There was no specific clinical manifestation that could help the diagnosis, which was made in 69.7% by histopathological analysis of brain tissue.

Conclusions
Seizures are a non-specific symptom to diagnose patients with cerebral schistosomiasis and accurate clinical indicators need to be derived through further studies.
Is There a Role for Perioperative Pelvic Radiotherapy in Surgically Resected Stage IV Rectal Cancer?
Authors: Kwon Jeanny , Kim Jun-Sang , Kim Byoung Hyuck 
Published: May 2021

Objectives:
This study aimed to determine whether perioperative pelvic radiotherapy (RT) improves outcomes in stage IV rectal cancer patients treated with primary surgical resection and systemic chemotherapy and to identify predictive factors for selection of patients for these approaches.

Materials and Methods:
We searched the Surveillance, Epidemiology, and End Results (SEER) database for patients diagnosed between 2010 and 2015 with stage IV rectal cancer, but without brain or bone metastases. After applying the exclusion criteria, a total of 26,132 patients were included in the analysis; propensity score matching was used to balance their individual characteristics.

Results:
Overall, 3283 (12.6%) patients received perioperative RT; the 3-year overall survival (OS) rates were 43.6% in the surgery group and 50.5% in the surgery with RT group (P<0.001). The survival benefit of RT was maintained after propensity score matching and multivariate adjustment (hazard ratio: 0.70; 95% confidence interval: 0.66-0.81; P<0.001). Interaction testing of the prognostic variables showed a significant interaction between RT and the presence of lung metastasis (P<0.001): the benefit of RT was observed only in patients without lung metastases (3 y OS 52.1% vs. 44.1%, P<0.001), but it was observed regardless of liver metastases. In addition, we developed a web-based calculator (http://bit.do/mRC_surv) to provide individualized estimates of OS benefit based on the receipt of perioperative pelvic RT.

Conclusions:
Perioperative pelvic RT significantly improved OS rates, especially in patients without lung metastases. We successfully developed a nomogram and web-based calculator that could predict survival benefit with the addition of RT for these patients.
Bayesian Forecasting for Intravenous Tobramycin Dosing in Adults With Cystic Fibrosis Using One Versus Two Serum Concentrations in a Dosing Interval
Authors: Drennan Philip G. , Thoma Yann , Barry Lucinda , Matthey Johan , Sivam Sheila , van Hal Sebastiaan J. 
Published: May 2021

Background:
Intravenous tobramycin treatment requires therapeutic drug monitoring (TDM) to ensure safety and efficacy when used for prolonged treatment, as in infective exacerbations of cystic fibrosis. The 24-hour area under the concentration–time curve (AUC24) is widely used to guide dosing; however, there remains variability in practice around methods for its estimation. The objective of this study was to determine the potential for a sparse-sampling strategy using a single postinfusion tobramycin concentration and Bayesian forecasting to assess the AUC24 in routine practice.

Methods:
Adults with cystic fibrosis receiving once-daily tobramycin had paired concentrations measured 2 hours (c1) and 6 hours (c2) after the end of infusion as routine monitoring. AUC24 exposures were estimated using Tucuxi, a Bayesian forecasting application that incorporates a validated population pharmacokinetic model. Simulations were performed to estimate AUC24 using the full data set using c1 and c2, compared with estimates using depleted data sets (c1 or c2 only), with and without concentration data from earlier in the course. The agreement between each simulation condition and the reference was assessed graphically and numerically using the median difference (∆) AUC24 and (relative) root mean square error (rRMSE) as measures of bias and accuracy, respectively.

Results:
A total of 55 patients contributed 512 concentrations from 95 tobramycin courses and 256 TDM episodes. Single concentration methods performed well, with median ∆AUC24 <2 mg·h·L−1 and rRMSE of <15% for sequential c1 and c2 conditions.

Conclusions:
Bayesian forecasting implemented in Tucuxi, using single postinfusion concentrations taken 2–6 hours after tobramycin administration, yield similar exposure estimates to more intensive (two-sample) methods and are suitable for routine TDM practice.