bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of AYC-SENSITIVE® for Rapid Detection of Multi-Drug Resistance and Extensively- Drug Resistance in Mycobacterium tuberculosis Isolates
Authors: Yıldırım Kübra , Ataş Cemilenur , Şimşek Ece , Çoban Ahmet Yılmaz 
Published: September 2022

Abstract
This study aimed to evaluate the AYC-SENSITIVE® kit for rapid detection of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) isolates. With the AYC-SENSITIVE® kit, a total of 36 isolates for susceptibility testing were evaluated (5 of which are standard (M. tuberculosis H37Rv; ATCC35822 (INH-resistant); ATCC35838 (RIF-resistant); ATCC35820 (STR-resistant) and ATCC35837 (EMB-resistant)) and 31 of which are clinic isolates). Susceptibility results were compared with the nitrate reductase test in Middlebrook 7H9 broth and the BACTEC MGIT 960 system which is the reference method. When the results were compared with the reference method, sensitivities were 100, 95, 100, 100%; specificities were 100, 100, 100, 92.86%; positive predictive values were (PPV) 100, 100, 100, 95.65%; negative predictive values (NPV) were 100, 94.12, 100, 100%, and the agreements were 100, 97.22, 100, 97.22% for INH, RIF, EMB, STR, respectively. Antibiotic susceptibility results with AYC-SENSITIVE® were obtained on the 5th day of incubation for 33 isolates and the 14th day of incubation for 3 isolates. Our results show that AYC-SENSITIVE® is a rapid kit that can be used in routine studies in laboratories suitable for tuberculosis for the early detection of MDR-TB and XDR-TB.
A versatile approach to evaluate the occurrence of microfibers in mussels Mytilus galloprovincialis from the Tyrrhenian Sea
Authors: Volgare Michela , Santonicola Serena , Cocca Mariacristina , Avolio Roberto , Castaldo Rachele , Errico Maria Emanuela , Gentile Gennaro , Raimo Gennaro , Gasperi Maurizio , Colavita Giampaolo 
Published: September 2022

Abstract
Microplastic of fibrous shape are esteemed to be the most abundant micro-debris form present in the environment, and considered a ubiquitous microplastic pollution that was recognized as a potential environmental stressor. In this study, a versatile approach to evaluate the occurrence of microfibers is proposed, able to discriminate among natural and synthetic microfibers, in farmed mussels (Mytilus galloprovincialis) from the Tyrrhenian Sea. The approach was useful to determine that microfibers were present in 74% of mussel samples, with a mean number of 14.57 microfibers/individual, corresponding to 3.13 microfibers/g w.w.. A negative correlation between the size of analysed mussels and the amount of microfibers/g w.w. (r(48)=-.339, p = .016) was detected, showing that smaller specimens contained more microfibers than the larger ones. This work pave the way to further studies aimed to adequately assess the risk that microfibers may pose for marine biota, also considering the commercial value as seafood items of many species of the Mytilus genus and the potential implication for human health.
Towards More Generalizable and Accurate Sentence Classification in Medical Abstracts with Less Data
Authors: Hu Yan , Chen Yong , Xu Hua 
Published: September 2022

Abstract
Purpose: With the unprecedented growth of biomedical publications, it is important to have structured abstracts in bibliographic databases (i.e., PubMed), thus, to facilitate the information retrieval and knowledge synthesis in needs of researchers.
Methods: Here we propose a few-shot prompt learning-based approach to classify sentences in medical abstracts of randomized clinical trials (RCT) and observational studies (OS) to subsections of Introduction, Background, Methods, Results, and Conclusion, using an existing corpus of RCT (PubMed 200k/20k RCT) and a newly built corpus of OS (PubMed 20k OS). 5 manually designed templates in a combination of 4 BERT model variants were tested and compared to a previous Hierarchical Sequential Labeling Network architecture and traditional BERT-based sentence classification method.
Results: On the PubMed 200k and 20k RCT datasets, we achieved overall F1 scores of 0.9508 and 0.9401 respectively. Under few-shot settings, we demonstrated that only 20\% of training data is sufficient to achieve a comparable F1 score by the HSLN model (0.9266 by us and 0.9263 by HSLN). When trained on the RCT dataset, our method achieved a 0.9065 F1 score on the OS dataset. When trained on the OS dataset, our method achieved a 0.9203 F1 score on the RCT dataset.
Conclusion: We show that the prompt learning-based method outperformed the existing method, even when fewer training samples were used. Moreover, the proposed method shows better generalizability across two types of medical publications when compared with the existing approach.
Transcriptome wide identification of CDR family in Citrus latifolia and its expression during HLB infection
Authors: Rosa Felipe Roberto Flores-de la , González-Cruz Carlos , Adame-García Jacel , Chan-León Arianna , Santillán-Mendoza Ricardo , Santamaría Jorge M. , Estrella-Maldonado Humberto 
Published: September 2022

Abstract
Huanglongbing (HLB) is the most important disease in citrus production around the world. Currently, there are not HLB-resistant citrus species or genotypes, however, Persian lime (Citrus latifolia Tan.) has been reported as the most tolerant citrus species to this disease, but their molecular mechanisms of tolerance has not being characterized yet. In other citrus species, Poncirus trifoliate, it has been suggested that the overexpression of CDR genes is associated to HLB tolerance, therefore, the aim of this work was to identify CDR gene family members in the Persian lime transcriptome and to determine if the HLB infection induces their expression. A Bayesian approach was used to search transcripts with one or two catalytic domains, then, a non-weighted parsimony phylogeny for CDR genes was carried out with the selected transcripts from C latifolia, P. trifoliata and C. sinensis, to identify phylogenetic homologous. The corresponding encoded proteins were obtained from the selected genes, and the similarity among them was estimated using alignments, identity matrix, UPGMA and conserved motifs analysis. Once the ClCDR genes were identified, their expression was determined with the transcriptome data and validated by RT-PCR and qRT-PCR in tissues of asymptomatic and HBL-symptomatic leaves. 146 sequences with one or two catalytic domains, were found, and 7 CDR clades were recovered. Similarity analysis demonstrated that there is a complex relationship among CDR genes and proteins in the species used in the present study. Moreover, the transcriptome and qRT-PCR data showed that none of the ClCDRgenes were expressed, neither in healthy nor in HLB-infected Persian lime plants, except for the ClCDR8a gene, which showed high expression. However, no significant differences were found between the ClCDR8a REL values from symptomatic or non-symptomatic leaves. Our results demonstrated the presence of CDR genes in the Persian lime genome, however, they suggest that HLB tolerance is not correlated with the overexpression of this gene family in this species.
Robot-assisted Complex Urinary Tract Reconstruction Using Intestinal Segments: Redefining the Paradigm
Authors: KUSHWAHA SWAPNIL SINGH , KALRA SIDHARTHA , N DORAIRAJAN L , S SREERAG K , ALI MUJAHID , PURUSHOTHAMAN JITHESH , KHURANA CHIRANJEET SINGH 
Published: September 2022

Abstract
INTRODUCTION:
Complex urinary tract reconstruction has significantly advanced with the increasing use of robot-assisted procedures. Robotic surgery aims to achieve the same outcomes as open surgery while minimizing morbidity by causing less blood loss, faster postoperative recovery, and reducing complications. This article shares our technique, challenges encountered, and experience of robot-assisted complex urinary tract reconstruction using intestinal segments.
METHODOLOGY:
Between January 2020 to March 2022, 6 patients who underwent robot-assisted complex urinary tract reconstruction using intestinal segments at our centre were retrospectively reviewed. Demographic, clinical, and operative data were recorded. Patients underwent renal function tests, blood gas analysis, and radiographic imaging in the follow-up. Symptomatic and radiologic relief were the criteria for success.
RESULTS:
Out of 6 cases, three patients underwent ileal ureter replacement, two combined ileal ureter with augmentation ileo-cystoplasty and one augmentation ileo-cystoplasty alone. The mean age, estimated blood loss, length of hospital stay, and follow-up period were 32.6 years, 110 ± 13.1 mL, 7.0 ± 1.1days, and 11.3 months respectively. The indications for surgery were either benign ureteral stricture following lithotripsy or sequelae of genitourinary tuberculosis. No intra-operative complications were found. Clavien-Dindo grade-II and Grade-III were found in three and one patient, respectively. During follow-up, none had compromised renal function or acidosis.
CONCLUSION:
Robot-assisted complex urinary tract reconstruction using intestinal segments is safe and offers the advantages of minimally invasive techniques. Techniques demonstrated in this article make these reconstructions feasible with good surgical and clinical outcomes.
Hierarchical Group Lasso Regression for Efficiently Identifying Interactions in Healthcare Risk-Adjustment Models
Authors: Ray Monika , Zhao Sharon , Wang Sheng , Bohl Alex , Romano Patrick S. 
Published: September 2022

Abstract
Researchers use risk-adjustment models to account for severity of illness in comparing patient outcomes across hospitals. Researchers specify important features as main effects, but they ignore interaction effects or use stratification methods, to account for effect modification, despite its limitations resulting from the number of potential strata. The Agency for Healthcare Research and Quality Inpatient Quality Indicator (IQI) 11, Abdominal Aortic Aneurysm Repair Mortality, is stratified into four groups based on the type of repair and rupture. IQI 09, Pancreatic Resection Mortality Rate, is stratified into two groups based on the presence of pancreatic cancer. The variable performance of these models motivated design of better models. We used hierarchical group lasso regularisation (HGLR) to identify first-order interactions in patient discharge data used in the development of risk-standardised models. HGLR identified unsuspected but clinically meaningful interactions for IQI 11, which has a heterogeneous population, but not for IQI 09. Synergistic interactions, such as between hypertension and respiratory failure, suggest patients merit special attention in perioperative care. Antagonistic interactions, such as between shock at admission and chronic comorbidities, illustrate that naïve main effects models overpredict risk in key population subsets, leading to miscalibrated models that yield biased estimates of hospital performance. HGLR is a useful and necessary step to identify first-order interactions for the development of robust risk-adjustment models used by agencies and stakeholders to rank hospitals in the US.
Higher TOX（Thymocyte selection-associated high mobility group box）expression in tumor microenvironment predicts poor prognosis in patients with ovarian cancer
Authors: Li Sai , Yang Sifu , Hong Yupeng 
Published: September 2022

Abstract
Background
Ovarian cancer is one of the most lethal gynecologic malignancies with a dismal prognosis that poses a serious threat to human health, highlighting the need for more knowledge about what is required for identifying some biomarkers for early diagnosis, prediction of prognosis and disease monitoring. TOX, a critical transcription factor related to the development of malignancies that contributing to lymphocytes not just T cells, had been proved prognostic value in some spectrum of cancers. Here, we aimed to study the prognostic role of TOX in ovarian cancer.
Results
We found that TOX was not only expressed in CD8 T cells but also tumor cells. TOX expression score was higher in ovarian cancer tissues and correlated with survival status. Survival analysis revealed that ovarian cancer patients with high TOX expression score generally shorter overall survival and disease-free survival times. Univariate and Multivariate Cox demonstrated that TOX expression score could be used as an independent prognostic factor for patients with ovarian cancer.
Conclusion
TOX expression in ovarian cancer could be a promising tool for predict overall survival of ovarian cancer patients.
Crop Models Improve Growth Simulation by Including Phenological Response to Water Stress
Authors: Mankin Kyle , Edmunds Debora , McMaster Gregory , Fox Fred , Wagner Larry , Green Timothy 
Published: September 2022

Abstract
Crop models can provide insights into the impacts of climate and management on crop growth and yield, but most currently are limited by overly simplistic assumptions about phenological development and response to water stress. We assessed winter wheat growth and yield performance of three crop models with lineage to the EPIC crop submodel. SWAT adopted the EPIC approach with few modifications, WEPS added new biomass accumulation, partitioning, and canopy approaches linked to key phenological development stages, and UPGM added to WEPS a detailed phenology component simulating responses to water stress. The models were evaluated with default parameters and compared to experimental data for winter wheat (Triticum aestivum L.) from two sites and a range of water-stress conditions for yield, aboveground biomass, biomass partitioning, canopy height, harvest index, and leaf area index. All models simulated yield very well (index of agreement [d] ≥ 0.93), but differences in model performance were increasingly evident for biomass (d = 0.91 [WEPS] to 0.86 [SWAT]), final canopy height (d = 0.68 [UPGM] to 0.44 [SWAT]), and harvest index (d = 0.61 [WEPS] to 0.43 [SWAT]). Errors in biomass simulation were most evident in the grain-filling period late in the growing season. Both WEPS and UPGM exhibited improved simulation of biomass and other response variables by including more explicit simulation of phenological response to water stress. The consistent improvement in winter wheat growth and yield simulation achieved with detailed phenology simulation provides an incentive to develop and test detailed phenology simulation components for other crops: currently 11 crops are simulated in UPGM, although the phenological parameters are uncalibrated. Better modeling linkages of water-stressed phenological development with other physiological processes will be critical to inform crop production where water stress and irrigation limitation are concerns.
On the Origin of Chemically Graded Metal/Ceramic Interface
Authors: Gollapalli Prince , Kishor PSVRA , Yadav Satyesh Kumar 
Published: September 2022

Abstract
A gradual variation in chemical composition at an atomic level in a metal/ceramic interface would result in a gradual variation in structural features that can give rise to unusual properties of the heterostructure. One of the ways such atomic-level chemical gradation can be achieved is by diffusion of anions from ceramic to metal. This process is perceived to be unfavorable because it requires the creation of anion vacancies in ceramic and anion interstitials in metal. We use the sum of C, N, or O vacancy formation energy in ceramics and their interstitial formation energy in metals to assess the possibility of migration of anions across the metal/ceramic interface, leading to an atomically chemically graded interface. We use the first-principles density functional theory to calculate the driving force for a few scientifically and technologically important metal/ceramic systems: a combination of 10 metals (M=Ti, Zr, Hf, V, Nb, Ta, Mg, Al, Cr, and Fe) and corresponding 30 ceramics MaXb (X=C, N, and O). The metal/ceramic systems that favor chemical gradation have metals from group IVB and VB mainly due to the large negative interstitial formation energies.
In vivo apatite-forming ability of second-generation hydraulic calcium silicate cements in rat subcutaneous tissue
Authors: Edanami Naoki , Takenaka Shoji , Belal Razi Saifullah Ibn , Yoshiba Kunihiko , Takahara Shintaro , Yoshiba Nagako , Ohkura Naoto , Noiri Yuichiro 
Published: September 2022

Abstract
Objectives
The objective of this study was to evaluate the in vivo apatite-forming ability of 17 second-generation hydraulic calcium silicate cements (HCSCs) with the first-generation HCSC, white ProRoot MTA (PR).
Materials and Methods
Seventeen second-generation HCSCs and PR were implanted in rat subcutaneous tissue for 28 days. After inplantation, Raman spectra were taken from the surface of the HCSC implants and blindly evaluated for the presence or absence of a band at 960 cm− 1 indicating apatite. Apatite formation was also assessed with surface characterization and elemental mapping.
Results
The Raman band for apatite was detected on only seven second-generation HCSCs and PR. These seven HCSCs exhibited apatite-like calcium- and phosphorus-rich spherical precipitates on their surface. Three types of HCSCs had a Raman band at 962 cm− 1 that may have obscured the Raman band for apatite at 960 cm− 1; however, elemental mapping demonstrated the absence of calcium-phosphorus-rich apatite-layer-like regions on these HCSCs.
Conclusions
Only 7 of the 17 second-generation HCSCs and PR produced apatite in vivo within 28 days.
Clinical Relevance:
The 10 types of second-generation HCSCs that did not exhibit apatite formation may not be suitable substitutes for PR due to their weak in vivo apatite-forming ability.
Complete genomic sequence of turnip mosaic virus infecting passionfruit in Fujian province of China
Authors: Li Xuefeng , Xie Lixue , Chen Xihong , Chen Jiangshan , Shen Jianguo , Gao Fangluan 
Published: September 2022

Abstract
The complete genome sequence of turnip mosaic virus (TuMV), isolated from diseased passion fruit (Passiflora edulia) in Fujian Province, China (TuMV-FJ) was determined. The viral genome was found to be 9,833 nucleotides in length excluding the poly(A) tail and to encode a polyprotein of 3164 amino acids, which was predicted to be cleaved into ten functional proteins by viral proteases. Phylogenetic analysis indicated that TuMV-FJ had closest phylogenetic relationship to BJ-B01, an isolate from Brassica oleracea in the world-B phylogenetic group of TuMV. Sequence analysis showed that TuMV-FJ shared more than 94% nucleotide and amino acid identities with BJ-B01. These results suggest that TuMV-FJ is a novel isolate of TuMV. To our knowledge, this is the first report of the complete genome sequence of TuMV infecting P. edulia.
Selective polyethylene glycol attachment to hemerythrin for potential use in blood substitutes
Authors: Arkosi Mariann-Kinga , Mot Augustin C. , Lupan Iulia , Tegla Miruna Georgiana Ghinia , Silaghi-Dumitrescu Radu 
Published: September 2022

Abstract
The oxygen carrying protein hemerythrin represents an alternative raw material to hemoglobin-based blood substitutes due to its reversible oxygen binding properties, relatively low redox reactivity and limited cytotoxicity. In order to increase the hydrodynamic volume and lower antigenicity, two site-directed variants, H82C and K92C, containing a single cysteine residue on the surface of each subunit of the hemerythrin octamer were engineered for specific attachment of polyethylene glycol (PEG). A sulfhydryl-reactive PEGylation reagent with a 51.9 Å spacer arm was employed for selective cysteine derivatization. The mutants were characterized by UV-vis spectroscopy, size-exclusion chromatography, oxygen affinity and autooxidation rate measurements. The H82C variant showed altered oligomeric behavior compared to the wild-type and was unstable in the met form. The PEGylated K92C variant was reasonably stable, displayed an oxygen affinity similar to that of the wild-type, and showed an increased rate of autoxidation; the latter disadvantage may be counteracted by further chemical modifications.
Realistic Scenarios of Pesticide Exposure Alters Multiple Biomarkers in Boana Pulchella (Anura) Adult Frogs
Authors: Pérez-Iglesias Juan Manuel , Natale Guillermo Sebastian , Brodeur Julie Celine , Larramendy Marcelo Luis 
Published: September 2022

Abstract
Imazethapyr, a post-emergent herbicide used in worldwide soybean and corn crops, induces genetic and biochemical alterations in aquatic vertebrates. This study examined relationship between biomarkers at different organization levels and imazethapyr real-life route exposure in Boana pulchella adults. Frogs were exposed to imazethapyr-based formulation Pivot® H (10.59%) at concentrations representing possible acute routes: field runoff (S1:10 mg.L− 1), direct foliar application with posterior frog presence (S2:100 mg.L− 1) and with frog presence (S3:1000 mg.L− 1). Post-exposure, endpoints levels were evaluated: organism alterations, biochemical activities and cytogenetic assays. Forty-eight hours post-exposure, antioxidant enzymes decrease, micronuclei induction and DNA damage were observed in all scenarios; while cholinesterase activity increase and body condition reduction were observed in frog-exposed to S3. Ninety-six hours post-exposure, frogs showed glutathione-S-transferase inhibition in S1, micronuclei induction in S2 and S3, and DNA-damage increase in S3. Herbicides routes of exposures in real-life could indicate that authorized applications have a risk to frogs populations.
Curcumin suppresses cell proliferation and reduces cholesterol absorption in Caco-2 cells by activating the TRPA1 channel
Authors: Qin Si , Su Qian , Li Xiang , Shao Muqing , Zhang Yindi , Yu Fadong , Ni Yinxing , Zhong Jian 
Published: September 2022

Abstract
Background: Curcumin (Cur) is a bioactive dietary polyphenol of turmeric with various biological activities against several cancers. Colorectal cancer (CRC) is one of the leading causes of cancer mortality worldwide. Intestinal cholesterol homeostasis is associated with CRC. A variety of side effects have been observed in patients with CRC because of treatment with chemotherapeutic drugs. Therefore, natural products can be an important strategy for potentially developing a com-plementary option for the primary prevention of CRC.
Methods: The present study used Cur as a therapeutic approach against CRC using the Caco-2 cell line. Based on the relative cell viability assessment up to a 100 μM concentration of Cur, a low-toxic concentration of 10 μM was adopted for further investigation.
Results: Cur inhibited cell proliferation in Caco-2 cells in a dose-dependent manner by activating the TRPA1 channel. Furthermore, the Cur-activated TRPA1 channel led to increased intracellular calcium, PPARγ upregulation, and the subsequent downregulation of the SP-1/SREBP-2/NPC1L1 signaling pathway-related proteins, and finally reduce cholesterol absorp-tion in Caco-2 cells.
Conclusions: Cur inhibits cell proliferation and reduces cholesterol absorption in Caco-2 cells through the Ca2+/PPARγ/SP-1/SREBP-2/NPC1L1 signaling by activating the TRPA1 channel, suggesting that Cur can be used as a dietary supplement for the primary prevention of CRC.