bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic review and meta-analysis of female lifestyle factors and risk of recurrent pregnancy loss
Authors: Ng Ka Ying Bonnie , Cherian George , Kermack Alexandra J. , Bailey Sarah , Macklon Nick , Sunkara Sesh K. , Cheong Ying 
Published: March 2021

AbstractIt is known that lifestyle factors affect sporadic miscarriage, but the extent of this on RPL (recurrent pregnancy loss) is less well known. A systematic review and meta-analysis was performed to assess the associations between lifestyle factors and RPL. Studies that analysed RPL in the context of BMI, smoking, alcohol and caffeine intake were included. The primary and secondary outcomes were odds of having RPL in the general population and odds of further miscarriage, respectively. Underweight and women with BMI > 25 are at higher odds of RPL in the general population (OR 1.2, 95% CI 1.12–1.28 and OR 1.21, 95% CI 1.06–1.38, respectively). In women with RPL, having BMI > 30 and BMI > 25 has increased odds of further miscarriages (OR 1.77, 95% CI 1.25–2.50 and OR 1.35, 95% CI 1.07–1.72, respectively). The quality of the evidence for our findings was low or very low. Being underweight and BMI > 25 contributes significantly to increased risk of RPL (general population). BMI > 25 or BMI > 30 increases the risk of further miscarriages (RPL population). Larger studies addressing the effects of alcohol, cigarette smoking and caffeine on the risk of RPL with optimisation of BMI in this cohort of women are now needed.
Hilbert–Schmidt speed as an efficient figure of merit for quantum estimation of phase encoded into the initial state of open n-qubit systems
Authors: Rangani Jahromi Hossein , Lo Franco Rosario 
Published: March 2021

AbstractHilbert–Schmidt speed (HSS) is a special type of quantum statistical speed which is easily computable, since it does not require diagonalization of the system state. We find that, when both HSS and quantum Fisher information (QFI) are calculated with respect to the phase parameter encoded into the initial state of an n-qubit register, the zeros of the HSS dynamics are actually equal to those of the QFI dynamics. Moreover, the signs of the time-derivatives of both HSS and QFI exactly coincide. These findings, obtained via a thorough investigation of several paradigmatic open quantum systems, show that HSS and QFI exhibit the same qualitative time evolution. Therefore, HSS reveals itself as a powerful figure of merit for enhancing quantum phase estimation in an open quantum system made of n qubits. Our results also provide strong evidence for both contractivity of the HSS under memoryless dynamics and its sensitivity to system-environment information backflows to detect the non-Markovianity in high-dimensional systems, as suggested in previous studies.
Temporal properties of higher-order interactions in social networks
Authors: Cencetti Giulia , Battiston Federico , Lepri Bruno , Karsai Márton 
Published: March 2021

AbstractHuman social interactions in local settings can be experimentally detected by recording the physical proximity and orientation of people. Such interactions, approximating face-to-face communications, can be effectively represented as time varying social networks with links being unceasingly created and destroyed over time. Traditional analyses of temporal networks have addressed mostly pairwise interactions, where links describe dyadic connections among individuals. However, many network dynamics are hardly ascribable to pairwise settings but often comprise larger groups, which are better described by higher-order interactions. Here we investigate the higher-order organizations of temporal social networks by analyzing five publicly available datasets collected in different social settings. We find that higher-order interactions are ubiquitous and, similarly to their pairwise counterparts, characterized by heterogeneous dynamics, with bursty trains of rapidly recurring higher-order events separated by long periods of inactivity. We investigate the evolution and formation of groups by looking at the transition rates between different higher-order structures. We find that in more spontaneous social settings, group are characterized by slower formation and disaggregation, while in work settings these phenomena are more abrupt, possibly reflecting pre-organized social dynamics. Finally, we observe temporal reinforcement suggesting that the longer a group stays together the higher the probability that the same interaction pattern persist in the future. Our findings suggest the importance of considering the higher-order structure of social interactions when investigating human temporal dynamics.
Effects of bioactive glass incorporation into glass ionomer cement on demineralized dentin
Authors: Kim Hyun-Jung , Bae Han Eul , Lee Ji-Eun , Park In-Seong , Kim Hee-Gyun , Kwon Jiyoung , Kim Duck-Su 
Published: March 2021

AbstractThe effects of the incorporation of sodium-free bioactive glass into glass ionomer cement (GIC) on the demineralized dentin are studied. Four experimental groups with various amounts of BAG in GIC were considered: BG0 group: 0 wt% (control); BG5 group: 5 wt%; BG10 group: 10 wt%; BG20 group: 20 wt%. The GIC surface and GIC-approximated demineralized dentin surfaces were evaluated using field emission scanning electron microscopy (FE–SEM). X-ray diffraction (XRD) analysis was performed to evaluate the chemical changes in the GIC-approximated dentin surface. In addition, a shear bond strength test was performed to evaluate the effects of BAG incorporation on the bond strength of GIC. FE–SEM analysis indicated that BAG-incorporated GICs formed distinct precipitates on their surface. Precipitates were also formed on the GIC-approximated demineralized dentin surface. It was more obvious when the amount of BAG increased. In the XRD analysis, fluorapatitie (FAP) peaks were detected in the BG5, BG10, and BG20 groups. There was no significant difference in the shear bond strength among all experimental groups. BAG-incorporated GIC precipitated FAP crystals underlying demineralized dentin surface without affecting bond strength. This study suggests the possibility of BAG as a beneficial additive in GIC.
Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow
Authors: de Mello Malta Fernanda , Amgarten Deyvid , Val Felipe Camilo , Cervato Murilo Castro , de Azevedo Bruna Mascaro Cordeiro , de Souza Basqueira Marcela , dos Santos Alves Camila Oliveira , Nobrega Maria Soares , de Souza Reis Rodrigo , Sebe Pedro , Gretschischkin Michel Chieregato , de Oliveira Diego Delgado Colombo , Nakamura Carolina Naomi Izo , Chazanas Pedro Lui Nigro , Pinho João Renato Rebello 
Published: March 2021

AbstractSince the first reported case of the new coronavirus infection in Wuhan, China, researchers and governments have witnessed an unseen rise in the number of cases. Thanks to the rapid work of Chinese scientists, the pathogen now called SARS-CoV-2 has been identified and its whole genome was deposited in public databases by early January 2020. The availability of the genome has allowed researchers to develop Reverse Transcription—Polymerase Chain Reaction (RT-PCR) assays, which are now the gold-standard for molecular diagnosis of the respiratory syndrome COVID19. Because of the rising number of cases and rapid spreading, the world has been facing a shortage of RT-PCR supplies, especially the ones involved in RNA extraction. This has been a major bottleneck to increase testing capacity in many countries that do not significantly manufacture these supplies, such as Brazil. Additionally, RT-qPCR scalability is highly dependent on equipment that usually performs testing of 96 samples at a time. In this work, we describe a cost-effective molecular NGS-based test for diagnosis of COVID19, which uses a single-step RNA extraction and presents high scalability and accuracy when compared to the gold-standard RT-qPCR. A single run of the NGS-based test using the Illumina NextSeq 550 mid-end sequencing equipment is able to multiplex 1,536 patient’s samples, providing individual semi-qualitative results (detected, not detected). Detected results are provided with fragments per million (FPM) values, which was demonstrated to correlate with RT-qPCR Cycle Threshold (CT) values. Besides, usage of the high-end Illumina Novaseq platform may yield diagnostic for up to 6144 samples in a single run. Performance results when compared with RT-qPCR show general accuracy of 96%, and 98% when only samples with CT values (gene N) lower than 30 are considered. We have also developed an online platform, termed VarsVID, to help test executors to easily scale testing numbers. Sample registering, wet-lab worksheets generation, sample sheet for sequencing and results’ display are all features provided by VarsVID. Altogether, these results will contribute to control COVID19 pandemics.
Molecular mechanisms of esophageal epithelial regeneration following repair of surgical defects with acellular silk fibroin grafts
Authors: Gundogdu Gokhan , Tosun Mehmet , Morhardt Duncan , Gheinani Ali Hashemi , Algarrahi Khalid , Yang Xuehui , Costa Kyle , Alegria Cinthia Galvez , Adam Rosalyn M. , Yang Wei , Mauney Joshua R. 
Published: March 2021

AbstractConstructive remodeling of focal esophageal defects with biodegradable acellular grafts relies on the ability of host progenitor cell populations to repopulate implant regions and facilitate growth of de novo functional tissue. Intrinsic molecular mechanisms governing esophageal repair processes following biomaterial-based, surgical reconstruction is largely unknown. In the present study, we utilized mass spectrometry-based quantitative proteomics and in silico pathway evaluations to identify signaling cascades which were significantly activated during neoepithelial formation in a Sprague Dawley rat model of onlay esophagoplasty with acellular silk fibroin scaffolds. Pharmacologic inhibitor and rescue experiments revealed that epithelialization of neotissues is significantly dependent in part on pro-survival stimuli capable of suppressing caspase activity in epithelial progenitors via activation of hepatocyte growth factor receptor (c-MET), tropomyosin receptor kinase A (TrkA), phosphoinositide 3-kinase (PI3K), and protein kinase B (Akt) signaling mechanisms. These data highlight the molecular machinery involved in esophageal epithelial regeneration following surgical repair with acellular implants.
Ab initio determination of crystal stability of di-p-tolyl disulfide
Authors: Hao Xuan , Liu Jinfeng , Ali Imran , Luo Hongyuan , Han Yanqiang , Hu Wenxin , Liu Jinyun , He Xiao , Li Jinjin 
Published: March 2021

AbstractWith the rapid growth of energy demand and the depletion of existing energy resources, the new materials with superior performances, low costs and environmental friendliness for energy production and storage are explored. Di-p-tolyl disulfide (p-Tol2S2) is a typical lubricating material, which has been applied in the field of energy storage. The conformational properties and phase transformations of p-Tol2S2 have been studied by pioneers, but their polymorphs and the polymorphism induced crystal structure changes require further analysis. In this study, we perform the crystal structural screening, prediction and optimization of p-Tol2S2 crystal with quantum mechanical calculations, i.e., density functional theory (DFT) and second-order Møller–Plesset perturbation (MP2) methods. A series of crystal structures with different molecular arrangements are generated based on the crystal structure screening. As compared to long-established lattice energy calculation, we take an advantage of using more accurate technique, which is Gibbs free energy calculation. It considers the effects of entropy and temperature to predict the crystal structures and energy landscape. By comparing the Gibbs free energies between predicted and experimental structures, we found that phase α is the most stable structure for p-Tol2S2 crystal at ambient temperature and standard atmospheric pressure. Furthermore, we provide an efficient method to discriminate different polymorphs that are otherwise difficult to be identified based on the Raman/IR spectra. The proposed work enable us to evaluate the quality of various crystal polymorphs rapidly.
Development and evaluation of a deep neural network for histologic classification of renal cell carcinoma on biopsy and surgical resection slides
Authors: Zhu Mengdan , Ren Bing , Richards Ryland , Suriawinata Matthew , Tomita Naofumi , Hassanpour Saeed 
Published: March 2021

AbstractRenal cell carcinoma (RCC) is the most common renal cancer in adults. The histopathologic classification of RCC is essential for diagnosis, prognosis, and management of patients. Reorganization and classification of complex histologic patterns of RCC on biopsy and surgical resection slides under a microscope remains a heavily specialized, error-prone, and time-consuming task for pathologists. In this study, we developed a deep neural network model that can accurately classify digitized surgical resection slides and biopsy slides into five related classes: clear cell RCC, papillary RCC, chromophobe RCC, renal oncocytoma, and normal. In addition to the whole-slide classification pipeline, we visualized the identified indicative regions and features on slides for classification by reprocessing patch-level classification results to ensure the explainability of our diagnostic model. We evaluated our model on independent test sets of 78 surgical resection whole slides and 79 biopsy slides from our tertiary medical institution, and 917 surgical resection slides from The Cancer Genome Atlas (TCGA) database. The average area under the curve (AUC) of our classifier on the internal resection slides, internal biopsy slides, and external TCGA slides is 0.98 (95% confidence interval (CI): 0.97–1.00), 0.98 (95% CI: 0.96–1.00) and 0.97 (95% CI: 0.96–0.98), respectively. Our results suggest that the high generalizability of our approach across different data sources and specimen types. More importantly, our model has the potential to assist pathologists by (1) automatically pre-screening slides to reduce false-negative cases, (2) highlighting regions of importance on digitized slides to accelerate diagnosis, and (3) providing objective and accurate diagnosis as the second opinion.
Stachyose triggers apoptotic like cell death in drought sensitive but not resilient plants
Authors: Okemo Pauline , Long Hao , Cheng Yen , Mundree Sagadevan , Williams Brett 
Published: March 2021

AbstractProgrammed cell death (PCD) is one of the most intensively researched fields in modern mammalian biology with roles in cancer, aging, diabetes and numerous neurodegenerative diseases. It is becoming increasingly clear that PCD also plays significant roles in plant defence and responses to the environment. Given their unique ability to tolerate desiccation (cells remain viable even after they’ve lost 95% of their water), resurrection plants make ideal models to study the regulation of plant PCD pathways. Previously, we showed that the Australian resurrection plant, Tripogon loliiformis, suppresses plant PCD, via trehalose-mediated activation of autophagy pathways, during drying. In the present study, we created a full-length T. loliiformis cDNA library, performed a large-scale Agrobacterium screen for improved salinity tolerance and identified Stachyose synthase (TlStach) as a potential candidate for improving stress tolerance. Tripogon loliiformis shoots accumulate stachyose synthase transcripts and stachyose during drying. Attempts to generate transgenic plants expressing TlStach failed and were consistent with previous reports in mammals that demonstrated stachyose-mediated induction of apoptosis. Using a combination of transcriptomics, metabolomics and cell death assays (TUNNEL and DNA laddering), we investigated whether stachyose induces apoptotic-like cell death in T. loliiformis. We show that stachyose triggers the formation of the hallmarks of plant apoptotic-like cell death in the desiccation sensitive Nicotiana benthamiana but not the resilient T. loliiformis. These findings suggest that T. loliiformis suppresses stachyose-mediated apoptotic-like cell death and provides insights on the role of sugar metabolism and plant PCD pathways. A better understanding of how resilient plants regulate sugar metabolism and PCD pathways may facilitate future targeting of plant metabolic pathways for increased stress tolerance.
Effects from the induction of heat shock proteins in a murine model due to progression of aortic atherosclerosis
Authors: Hashikawa Naoya , Ido Masanobu , Morita Yuna , Hashikawa-Hobara Narumi 
Published: March 2021

AbstractHeat shock proteins (HSPs) are molecular chaperones that repair denatured proteins. The relationship between HSPs and various diseases has been extensively studied. However, the relationship between HSPs and atherosclerosis remains unclear. In this study, we induced the expression of HSPs and analyzed the effects on the development/progression of atherosclerosis in vivo. Remarkably, when HSPs were induced in apolipoprotein E deficient (ApoE−/−) mice prior to the formation of atheromas, the progression of atherosclerosis was inhibited; the short-term induction of HSPs significantly decreased the mRNA expression of intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) in the aorta. In contrast, the induction of HSPs after the formation of atheromas promoted the progression of atherosclerosis. In fact, the short-term induction of HSPs, after the formation of atheromas, significantly increased the mRNA expression of tumor necrosis factor-alpha, and interleukin 6 in the aorta. Of note, the induction of HSPs also promoted the formation of macrophage-derived foam cells. Overall, these results indicate that HSPs exerts different effects in the context of aortic atherosclerosis, depending on its degree of progression. Therefore, the induction and inhibition of HSPs should be considered for the prevention and treatment of atherosclerosis, respectively.
Subtle cardiac dysfunction in lymphoma patients receiving low to moderate dose chemotherapy
Authors: Chang Hsien-Yuan , Lee Chun-Hui , Su Po-Lan , Li Sin-Syue , Chen Ming-Yueh , Chen Ya-Ping , Hsu Ya-Ting , Tsai Wei-Chuan , Liu Ping-Yen , Chen Tsai-Yun , Liu Yen-Wen 
Published: March 2021

AbstractLeft ventricular (LV) global peak systolic longitudinal strain (GLS) is a sensitive measurement for detecting subtle LV systolic dysfunction and a powerful prognostic predictor. However, the clinical implication of LV GLS in lymphoma patients receiving cancer therapy remains unknown. We prospectively enrolled 74 lymphoma patients (57.9 ± 17.0 years old, 57% male). We performed echocardiographic studies after the 3rd and 6th cycles and 1 year after chemotherapy and a cardiopulmonary exercise test upon completion of 3 cycles of anticancer therapy. Cancer therapy-related cardiac dysfunction (CTRCD) was defined as a ≥ 15% relative reduction in GLS value from baseline. The primary outcome was a composite of all-cause mortality and heart failure events. Thirty-six patients (49%) had CTRCD (LV GLS: baseline vs. after 3rd cycle of therapy: 20.1 ± 2.6 vs. 17.5 ± 2.3%, p < 0.001). CTRCD was detected after the 3rd cycle of anticancer therapy. CTRCD patients had impaired exercise capacity (minute oxygen consumption/kg, CTRCD vs. CTRCD (-): 13.9 ± 3.1 vs. 17.0 ± 3.9 ml/kg/min, p = 0.02). More primary outcome events occurred in the CTRCD group (hazard ratio 3.21; 95% confidence interval 1.04–9.97; p = 0.03). LV GLS could detect subtle but clinically significant cardiac dysfunction in lymphoma patients in the early stage of anticancer therapy. CTRCD may be associated with not only a reduced exercise capacity but also a worse prognosis.
A novel scoring system for TIGIT expression in classic Hodgkin lymphoma
Authors: Annibali Ombretta , Bianchi Antonella , Grifoni Alba , Tomarchio Valeria , Tafuri Mariantonietta , Verri Martina , Avvisati Giuseppe , Crescenzi Anna 
Published: March 2021

AbstractClinical use of immune-checkpoints inhibitors (anti PD-1/PD-L1) resulted very effective for the treatment of relapsed/refractory classic Hodgkin Lymphoma (CHL). Recently, T cell Ig and ITIM domains (TIGIT) has been recognized as an immune checkpoint receptor able to negatively regulate T cell functions. Herein, we investigated the expression of TIGIT in CHL microenvironment in order to find a potential new target for inhibitor therapy. TIGIT, PD-1 and PD-L1 expression was evaluated in 34 consecutive patients with CHL. TIGIT expression in T lymphocytes surrounding Hodgkin Reed-Sternberg (HRS) cells was observed in 19/34 patients (56%), of which 11 (58%) had advanced stages. In 16/19 (84%) cases, TIGIT+ peritumoral T lymphocytes showed also PD-1 expression. All 15 TIGIT− patients had PD-L1 expression in HRS cells (100%) while among 19 TIGIT+ patients, 11 (58%) were PD-L1+ and 8 (42%) were PD-L1−. Using a new scoring system for TIGIT immunoreactivity, all TIGIT+ cases with higher score (4/19) were PD-L1−. Our results confirm co-expression of TIGIT and PD-1 in peritumoral T lymphocytes. Of relevance, we demonstrated a mutually exclusive expression of TIGIT and PD-L1 using new TIGIT scoring system able to identify this immunocheckpoints’ modulation. These results pave the way to new therapeutic strategies for relapsed/refractory CHL.
A prospective, observational clinical trial on the impact of COVID-19-related national lockdown on thyroid hormone in young males
Authors: Brigante Giulia , Spaggiari Giorgia , Rossi Barbara , Granata Antonio , Simoni Manuela , Santi Daniele 
Published: March 2021

AbstractTrying to manage the dramatic coronavirus disease 2019 (COVID-19) infection spread, many countries imposed national lockdown, radically changing the routinely life of humans worldwide. We hypothesized that both the pandemic per se and the consequent socio-psychological sequelae could constitute stressors for Italian population, potentially affecting the endocrine system. This study was designed to describe the effect of lockdown-related stress on the hypothalamic-pituitary-thyroid (HPT) axis in a cohort of young men. A prospective, observational clinical trial was carried out, including patients attending the male infertility outpatient clinic before and after the national lockdown for COVID-19 pandemic. The study provided a baseline visit performed before and a follow-up visit after the lockdown in 2020. During the follow-up visit, hormonal measurements, lifestyle habits and work management were recorded. Thirty-one male subjects were enrolled (mean age: 31.6 ± 6.0 years). TSH significantly decreased after lockdown (p = 0.015), whereas no significant changes were observed in the testosterone, luteinising hormone, follicle-stimulating hormone, estradiol and prolactin serum levels. No patient showed TSH serum levels above or below reference ranges, neither before nor after lockdown. Interestingly, TSH variation after lockdown was dependent on the working habit change during lockdown (p = 0.042). We described for the first time a TSH reduction after a stressful event in a prospective way, evaluating the HPT axis in the same population, before and after the national lockdown. This result reinforces the possible interconnection between psychological consequences of a stressful event and the endocrine regulation.