bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting the single-cell transcriptome network in patients with esophageal squamous cell carcinoma receiving operative paclitaxel plus platinum chemotherapy
Authors: Chen Zhencong , Huang Yiwei , Hu Zhengyang , Zhao Mengnan , Bian Yunyi , Chen Zongwei , Zheng Yuansheng , Bi Guoshu , Pang Yanrui , Zhan Cheng , Lin Zongwu , Guo Weigang , Wang Qun , Tan Lijie 
Published: October 2021

AbstractEsophageal squamous cell carcinoma (ESCC) accounts for 90% of all cases of esophageal cancers worldwide. Although neoadjuvant chemotherapy (NACT-ESCC) improves the survival of ESCC patients, the five-year survival rate of these patients is dismal. The tumor microenvironment (TME) and tumor heterogeneity decrease the efficacy of ESCC therapy. In our study, 113,581 cells obtained from five ESCC patients who underwent surgery alone (SA-ESCC) and five patients who underwent preoperative paclitaxel plus platinum chemotherapy (NACT-ESCC), were used for scRNA-seq analysis to explore molecular and cellular reprogramming patterns. The results showed samples from NACT-ESCC patients exhibited the characteristics of malignant cells and TME unlike samples from SA-ESCC patients. Cancer cells from NACT-ESCC samples were mainly at the ‘intermediate transient stage’. Stromal cell dynamics showed molecular and functional shifts that formed the immune-activation microenvironment. APOE, APOC1, and SPP1 were highly expressed in tumor-associated macrophages resulting in anti-inflammatory macrophage phenotypes. Levels of CD8+ T cells between SA-ESCC and NACT-ESCC tissues were significantly different. Immune checkpoints analysis revealed that LAG3 is a potential immunotherapeutic target for both NACT-ESCC and SA-ESCC patients. Cell–cell interactions analysis showed the complex cell-cell communication networks in the TME. In summary, our findings elucidate on the molecular and cellular reprogramming of NACT-ESCC and ESCC patients. These findings provide information on the potential diagnostic and therapeutic targets for ESCC patients.
Lifestyle considerations in multiple myeloma
Authors: Shapiro Yael N. , Peppercorn Jeffrey M. , Yee Andrew J. , Branagan Andrew R. , Raje Noopur S. , Donnell Elizabeth K. O’ 
Published: October 2021

AbstractAs the prognosis for multiple myeloma (MM) has significantly improved and patients remain on therapy longer, there is a need for supportive care interventions to optimize patient quality of life (QOL) and functional status over the course of cancer treatment. MM is characterized by a significant symptom burden and a relatively lower QOL compared to other cancers. This review evaluates the role of healthy lifestyle behaviors in improving both the physical functioning and psychological well-being of the MM population. We (1) describe the current literature on physical activity, weight management, diet, sleep, and substance use in the context of MM, (2) present important considerations for incorporating lifestyle factors into clinical practice, and (3) identify directions for future research. Developing MM-specific guidelines for modifiable lifestyle changes that take into account both the length of treatment and the unique disease features (i.e. osteolytic lesions and anemia) may provide a promising path for improved patient QOL and functioning.
Type V collagen alpha 1 chain promotes the malignancy of glioblastoma through PPRC1-ESM1 axis activation and extracellular matrix remodeling
Authors: Tsai Hsing-Fang , Chang Yu-Chan , Li Chien-Hsiu , Chan Ming-Hsien , Chen Chi-Long , Tsai Wen-Chiuan , Hsiao Michael 
Published: October 2021

AbstractGlioblastoma (GBM) is a fatal cancer. Existing therapies do not have significant efficacy for GBM patients. Previous studies have shown that the collagen family is involved in the regulation of the extracellular environment of cancer cells, and these conditions could become an important factor for effective treatment. Therefore, we screened various collagen types and observed that the type V collagen α1 chain (COL5A1) gene plays a pivotal role in GBM. We further examined whether the overexpression of COL5A1 is common in mesenchymal subtypes and is related to the survival rate of GBM patients through several in silico cohorts. In addition, our cohort also showed a consistent trend in COL5A1 protein levels. Most importantly, we validated the cell mobility, metastatic ability and actin polymerization status caused by COL5A1 with two-way models. Based on these results, we established a transcriptomics dataset based on COL5A1. Moreover, PPRC1, GK and ESM1 were predicted by ingenuity pathway analysis (IPA) to be transcription factors or to participate downstream. We investigated the involvement of COL5A1 in extracellular remodeling and the regulation of actin filaments in the metastasis of GBM. Our results indicate that the COL5A1−PPRC1−ESM1 axis may represent a novel therapeutic target in GBM.
Two novel Warburg micro syndrome 1 cases caused by pathogenic variants in RAB3GAP1
Authors: Alavi Omid , Khamirani Hossein Jafari , Zoghi Sina , Feili Afrooz , Dastgheib Seyed Alireza , Tabei Seyed Mohammad Bagher , Manoochehri Jamal , Panahandeh Seyed Mehdi , Kamali Majid , Dianatpour Mehdi 
Published: October 2021

AbstractIn this study, we detected a novel pathogenic variant and a previously reported variant in RAB3GAP1 by whole-exome sequencing (NM_001172435.2: c.1552C>T, p.Gln518*; c.1471C>T, p.Arg491*). The first patient is a 3-year-old girl who presented with bilateral congenital cataracts, developmental delay, abnormal craniofacial features, drug-resistant constipation, and corpus callosum hypoplasia. The proband of the second family is a 13-year-old boy who suffers from developmental delay, quadriplegia, intellectual disability, abnormal craniofacial features, and corpus callosum hypoplasia.
Distinct behavior of the little finger during the vertical translation of an unsteady thumb platform while grasping
Authors: Banuvathy Rajakumar , Varadhan SKM 
Published: October 2021

AbstractObject stabilization while grasping is a common topic of research in motor control and robotics. Forces produced by the peripheral fingers (index and little) play a crucial role in sustaining the rotational equilibrium of a handheld object. In this study, we examined the contribution of the peripheral fingers towards object stabilization when the rotational equilibrium is disturbed. For this purpose, the thumb was placed over an unsteady platform and vertically translated. The task was to trace a trapezoid or an inverted trapezoid pattern by moving the thumb platform in the vertical direction. The thumb displacement data served as visual feedback to trace the pattern displayed. Participants were instructed to maintain the handle in static equilibrium at all times. We observed that the change in the normal force of the little finger due to the downward translation of the thumb was significantly greater than the change in the normal force of the index finger due to the upward translation. We speculate that morphological correlations (between thumb and little finger) during the displacement of the thumb might be a reason for such large increases in the little finger forces.
A haploscope based binocular pupillometer system to quantify the dynamics of direct and consensual Pupillary Light Reflex
Authors: Meethal Najiya S. K. , Mazumdar Deepmala , Morshchavka Sergii , Robben Jasper , van der Steen J. , George Ronnie , Pel Johan J. M. 
Published: October 2021

AbstractThis study described the development of a haploscope-based pupillometer for the parametrization of the Pupillary Light Reflex (PLR), and its feasibility in a set of 30 healthy subjects (light or dark-colored irides) and five patients diagnosed with Relative Afferent Pupillary Defect (RAPD). Our supplementary aim focused on evaluating the influence of iris colour on the PLR to decide whether a difference in PLR parameters should be anticipated when this system is used across ethnicities. All the participants underwent a customized pupillometry protocol and the generated pupil traces, captured by an eye tracker, were analyzed using exponential fits to derive PLR parameters. A Pupil Response Symmetry (PRS) coefficient was calculated to predict the presence of RAPD. The mean (SD) Initial PD during dilation (3.2 (0.5) mm) and the minimum PD during constriction (2.9 (0.4) mm) in the light iris group had a statistically significant (p < 0.001) higher magnitude compared to the dark iris group. The normal limits of the PRS coefficient ranged from − 0.20 to + 1.07 and all RAPD patients were outside the calculated normal limits. This proposed system, analysis strategies, and the tested metrics showed good short-term repeatability and the potential in detecting pupil abnormalities in neuro-ophthalmic diseases.
Pseudogenization of the chloroplast threonine (trnT-GGU) gene in the sunflower family (Asteraceae)
Authors: Abdullah  , Mehmood Furrukh , Heidari Parviz , Rahim Abdur , Ahmed Ibrar , Poczai Peter 
Published: October 2021

AbstractThe chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the chloroplast threonine (trnT-GGU) gene was previously reported in Cryptomeria japonica (Cupressaceae), Pelargonium × hortorum (Geraniaceae), and Anaphalis sinica and Leontopodium leiolepis of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of 13 subfamilies of Asteraceae and found this gene as a pseudogene in core Asteraceae (Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae), which was linked to an insertion event within the 5′ acceptor stem and is not associated with ecological factors such as habit, habitat, and geographical distribution of the species. The pseudogenization of trnT-GGU was not predicted in codon usage, indicating that the superwobbling phenomenon occurs in core Asteraceae in which a single transfer RNA (trnT-UGU) decodes all four codons of threonine. To the best of our knowledge, this is the first evidence of a complete clade of a plant species using the superwobbling phenomenon for translation.
Microclimate and the vertical stratification of potential bridge vectors of mosquito‑borne viruses captured by nets and ovitraps in a central Amazonian forest bordering Manaus, Brazil
Authors: Hendy Adam , Valério Danielle , Fé Nelson Ferreira , Hernandez-Acosta Eduardo , Mendonça Claudia , Andrade Eloane , Pedrosa Igor , Costa Edson Rodrigues , Júnior José Tenaçol Andes , Assunção Flamarion Prado , Chaves Bárbara Aparecida , Scarpassa Vera Margarete , Gordo Marcelo , Buenemann Michaela , de Lacerda Marcus Vinícius Guimarães , Hanley Kathryn A. , Vasilakis Nikos 
Published: October 2021

AbstractIn the Americas, some mosquito-borne viruses such as Zika, chikungunya, and dengue circulate among humans in urban transmission cycles, while others, including yellow fever and Mayaro, circulate among monkeys in sylvatic cycles. The intersection of humans and wildlife at forest edges creates risk for zoonotic virus exchange. We built a scaffold tower at the edge of a treefall gap in rainforest bordering Manaus, Brazil, to identify vectors that may bridge transmission between humans and monkeys. We vertically sampled diurnally active, anthropophilic mosquitoes using handheld nets at 0, 5, and 9 m and container-breeding mosquitoes in ovitraps at 0, 5, 10, and 15 m. Haemagogus janthinomys and Psorophora amazonica were present in high relative abundance in nets at each height sampled, while anthropophilic species were uncommon in ovitraps. Hg. janthinomys was more abundant at elevated heights than at ground level, while Ps. amazonica abundance was not significantly stratified across heights. The presence of each species increased with increasing 7-day rainfall lagged at 1 week, and at 1 and 4 weeks prior to collection, respectively. In addition, Hg. janthinomys was most frequently collected at 29.9 °C, irrespective of height. These data provide insight into the potential role of each species as bridge vectors.
The largest hoplophonine and a complex new hypothesis of nimravid evolution
Authors: Barrett Paul Zachary 
Published: October 2021

AbstractNimravids were the first carnivorans to evolve saberteeth, but previously portrayed as having a narrow evolutionary trajectory of increasing degrees of sabertooth specialization. Here I present a novel hypothesis about the evolution of this group, including a description of Eusmilus adelos, the largest known hoplophonine, which forces a re-evaluation of not only their relationships, but perceived paleoecology. Using a tip-dated Bayesian analysis with sophisticated evolutionary models, nimravids can now be viewed as following two paths of evolution: one led to numerous early dirk-tooth forms, including E. adelos, while the other converged on living feline morphology, tens of millions of years before its appearance in felids.
Quantum cryptographic resource distillation and entanglement
Authors: Choi Minjin , Lee Soojoon 
Published: October 2021

AbstractWe look into multipartite quantum states on which quantum cryptographic protocols including quantum key distribution and quantum secret sharing can be perfectly performed, and define the quantum cryptographic resource distillable rate as the asymptotic rate at which such multipartite state can be distilled from a given multipartite state. Investigating several relations between entanglement and the rate, we show that there exists a multipartite bound entangled state whose quantum cryptographic resource distillable rate is strictly positive, that is, there exists a multipartite entangled state which is not distillable, but can be useful for quantum cryptography such as quantum key distribution and quantum secret sharing.
Classifying diseases by using biological features to identify potential nosological models
Authors: Prieto Santamaría Lucía , García del Valle Eduardo P. , Zanin Massimiliano , Hernández Chan Gandhi Samuel , Pérez Gallardo Yuliana , Rodríguez-González Alejandro 
Published: October 2021

AbstractEstablished nosological models have provided physicians an adequate enough classification of diseases so far. Such systems are important to correctly identify diseases and treat them successfully. However, these taxonomies tend to be based on phenotypical observations, lacking a molecular or biological foundation. Therefore, there is an urgent need to modernize them in order to include the heterogeneous information that is produced in the present, as could be genomic, proteomic, transcriptomic and metabolic data, leading this way to more comprehensive and robust structures. For that purpose, we have developed an extensive methodology to analyse the possibilities when it comes to generate new nosological models from biological features. Different datasets of diseases have been considered, and distinct features related to diseases, namely genes, proteins, metabolic pathways and genetical variants, have been represented as binary and numerical vectors. From those vectors, diseases distances have been computed on the basis of several metrics. Clustering algorithms have been implemented to group diseases, generating different models, each of them corresponding to the distinct combinations of the previous parameters. They have been evaluated by means of intrinsic metrics, proving that some of them are highly suitable to cover new nosologies. One of the clustering configurations has been deeply analysed, demonstrating its quality and validity in the research context, and further biological interpretations have been made. Such model was particularly generated by OPTICS clustering algorithm, by studying the distance between diseases based on gene sharedness and following cosine index metric. 729 clusters were formed in this model, which obtained a Silhouette coefficient of 0.43.
Evaluation of a saliva molecular point of care for the detection of SARS-CoV-2 in ambulatory care
Authors: LeGoff Jérôme , Kernéis Solen , Elie Caroline , Mercier-Delarue Séverine , Gastli Nabil , Choupeaux Laure , Fourgeaud Jacques , Alby Marie-Laure , Quentin Pierre , Pavie Juliette , Brazille Patricia , Néré Marie Laure , Minier Marine , Gabassi Audrey , Leroy Chrystel , Parfait Béatrice , Tréluyer Jean-Marc , Delaugerre Constance 
Published: October 2021

AbstractRapid identification of SARS-CoV-2-infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swabs. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Overall, 117 of the 1718 participants (7%) tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97%, respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference tests, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. The detection of SARS-CoV-2 in crude saliva samples with an RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.Registration number: NCT04578509.
Murine SEC24D can substitute functionally for SEC24C during embryonic development
Authors: Adams Elizabeth J. , Khoriaty Rami , Kiseleva Anna , Cleuren Audrey C. A. , Tomberg Kärt , van der Ent Martijn A. , Gergics Peter , Tang Vi T. , Zhu Guojing , Hoenerhoff Mark J. , O’Shea K. Sue , Saunders Thomas L. , Ginsburg David 
Published: October 2021

AbstractThe COPII component SEC24 mediates the recruitment of transmembrane cargos or cargo adaptors into newly forming COPII vesicles on the ER membrane. Mammalian genomes encode four Sec24 paralogs (Sec24a-d), with two subfamilies based on sequence homology (SEC24A/B and C/D), though little is known about their comparative functions and cargo-specificities. Complete deficiency for Sec24d results in very early embryonic lethality in mice (before the 8 cell stage), with later embryonic lethality (E7.5) observed in Sec24c null mice. To test the potential overlap in function between SEC24C/D, we employed dual recombinase mediated cassette exchange to generate a Sec24cc-d allele, in which the C-terminal 90% of SEC24C has been replaced by SEC24D coding sequence. In contrast to the embryonic lethality at E7.5 of SEC24C-deficiency, Sec24cc-d/c-d pups survive to term, though dying shortly after birth. Sec24cc-d/c-d pups are smaller in size, but exhibit no other obvious developmental abnormality by pathologic evaluation. These results suggest that tissue-specific and/or stage-specific expression of the Sec24c/d genes rather than differences in cargo export function explain the early embryonic requirements for SEC24C and SEC24D.
The response of different kinds of rapeseed cultivars to foliar application of nitrogen, sulphur and boron
Authors: Sikorska Anna , Gugała Marek , Zarzecka Krystyna 
Published: October 2021

AbstractThe study was based on in 2016–2017, 2017–2018, 2018–2019 field experiment conducted at the University of Natural Sciences and Humanities in Siedlce (Zawady Agricultural Experimental Station), eastern Poland. The studied factors were: I. winter rape cultivars: Monolit—open pollinated cultivar; PT248-F1 hybrid cultivars with traditional growth type; PX115-F1 hybrid cultivars with a semi-dwarf growth type and types of foliar nutrition: (1) control variant without foliar nutrition and amino acids; (2) amino acid; (3) foliar fertilizer sulphur and boron; (4) foliar fertilizer sulphur with foliar fertilizer boron and amino acid. The aim of the study was to determine the effect of foliar application of sulphur, boron, amino acids on the use and feed value of seeds of three winter rape morphotypes. The highest content of crude fat in seeds of the studied morphotypes was found after foliar fertilization with sulphur and boron and amino acids, while the lowest under the influence of amino acids. The highest concentration of total protein was obtained after the application of amino acids, and regardless of the morphotype studied on this object, the same value of this trait was demonstrated. In restored morphotypes, the use of additional foliar fertilization S and B in combination with amino acids did not significantly increase this characteristic compared to the amino acid variant. As a result of the application of amino acids and foliar feeding of S and B, and amino acids, the largest increase in crude fibre content in rapeseeds was obtained, while the application of S and B did not significantly increase this characteristic compared to the control variant. The best feed and use value of seeds were noted in restored morphotypes, with the semi-dwarf variety having the highest fat and crude fibre content. Climatic conditions in the years of research significantly determined the value of seeds. The highest values of the examined traits were obtained in the last year of the study, and the lowest in the growing season 2016–2017.
Variable intraspecific space use supports optimality in an apex predator
Authors: Finnegan S. P. , Svoboda N. J. , Fowler N. L. , Schooler S. L. , Belant J. L. 
Published: October 2021

AbstractWithin optimality theory, an animal’s home range can be considered a fitness-driven attempt to obtain resources for survival and reproduction while minimizing costs. We assessed whether brown bears (Ursus arctos) in two island populations maximized resource patches within home ranges (Resource Dispersion Hypothesis [RDH]) or occupied only areas necessary to meet their biological requirements (Temporal Resource Variability Hypothesis [TRVH]) at annual and seasonal scales. We further examined how intrinsic factors (age, reproductive status) affected optimal choices. We found dynamic patterns of space use between populations, with support for RDH and TRVH at both scales. The RDH was likely supported seasonally as a result of bears maximizing space use to obtain a mix of nutritional resources for weight gain. Annually, support for RDH likely reflected changing abundances and distributions of foods within different timber stand classes. TRVH was supported at both scales, with bears minimizing space use when food resources were temporally concentrated. Range sizes and optimal strategies varied among sex and reproductive classes, with males occupying larger ranges, supporting mate seeking behavior and increased metabolic demands of larger body sizes. This work emphasizes the importance of scale when examining animal movement ecology, as optimal behavioral decisions are scale dependent.