bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water Management Practices: Use Patterns, Related Factors, and Correlations With Irrigated Acres
Authors: Nian Yefan , Huang Qiuqiong , Kovacs Kent F. , Henry Christopher , Krutz Jason 
Published: February 2020

AbstractThis study describes the water management practice (WMP) use patterns by producers in Arkansas, USA, identifies the factors related to producers' choices among WMP groups, and examines the correlations between WMP uses and irrigated acreage. Using data from the 2016 Arkansas Irrigation Survey, WMPs are divided into four groups: field management, water flow control, water recovery/storage, and advanced irrigation scheduling practices. We find that about 77% of producers in the study area use two or more groups of WMPs to manage multiple aspects of irrigation, but that the factors that are associated with choices of WMPs vary by WMP group. Regression results show that the use of water flow meters, providing producers with education on the looming groundwater shortage problems and awareness of financial assistance available for conservation efforts, such as the state tax credits program, and use of WMPs by family members, friends, and neighbors are associated with increased use of WMPs. However, we find that producers that are older, have smaller farms, and rely more on groundwater are less likely to use some of the WMPs. Regression results also show that using water flow meters positively correlates with total irrigated acres, irrigated acres in rice, and irrigated acres in soybeans, and that for soybeans using more groups of WMPs is associated with a reduced extent of irrigated acreage. This study contributes to the small economics literature on WMPs and provides a more comprehensive picture of how producers use different WMPs to manage irrigation.
Validation of the IPSET score for thrombosis in patients with prefibrotic myelofibrosis
Authors: Guglielmelli Paola , Carobbio Alessandra , Rumi Elisa , De Stefano Valerio , Mannelli Lara , Mannelli Francesco , Rotunno Giada , Coltro Giacomo , Betti Silvia , Cavalloni Chiara , Finazzi Maria Chiara , Thiele Juergen , Cazzola Mario , Vannucchi Alessandro Maria , Barbui Tiziano 
Published: February 2020

AbstractPre-fibrotic myelofibrosis (pre-PMF) and essential thrombocythemia (ET) are characterized by similarly increased rate of thrombotic events, but no study specifically analyzed risk factors for thrombosis in pre-PMF. In a multicenter cohort of 382 pre-PMF patients collected in this study, the rate of arterial and venous thrombosis after diagnosis was 1.0 and 0.95% patients/year. Factors significantly associated with arterial thrombosis were age, leukocytosis, generic cardiovascular risk factors, JAK2V617F and high molecular risk mutations, while only history of previous thrombosis, particularly prior venous thrombosis, was predictive of venous events. The risk of total thromboses was accurately predicted by the the international prognostic score for thrombosis in essential thrombocythemia (IPSET) score, originally developed for ET, and corresponded to 0.67, 2.05, and 2.95% patients/year in the low-, intermediate-, and high-risk categories. IPSET was superior to both the conventional 2-tiered score and the revised IPSET in this cohort of pre-PMF patients. We conclude that IPSET score can be conveniently used for thrombosis risk stratification in patients with pre-PMF and might represent the basis for individualized management aimed at reducing the increased risk of major cardiovascular events. Further refinement of the IPSET score in pre-PMF might be pursued by additional, prospective studies evaluating the inclusion of leukocytosis and/or adverse mutational profile as novel variables.
Impact of panel design and cut-off on tumour mutational burden assessment in metastatic solid tumour samples
Authors:   CPCT Consortium, Mankor Joanne M. , Paats Marthe S. , Groenendijk Floris H. , Roepman Paul , Dinjens Winand N. M. , Dubbink Hendrikus J. , Sleijfer Stefan , Cuppen Edwin , Lolkema Martijn P. J. K. 
Published: February 2020

AbstractTumour mutational burden (TMB) has emerged as a promising biomarker to predict immune checkpoint inhibitors (ICIs) response in advanced solid cancers. However, harmonisation of TMB reporting by targeted gene panels is lacking, especially in metastatic tumour samples. To address this issue, we used data of 2841 whole-genome sequenced metastatic cancer biopsies to perform an in silico analysis of TMB determined by seven gene panels (FD1CDx, MSK-IMPACT™, Caris Molecular Intelligence, Tempus xT, Oncomine Tumour Mutation Load, NeoTYPE Discovery Profile and CANCERPLEX) compared to exome-based TMB as a golden standard. Misclassification rates declined from up to 30% to <1% when the cut-point for high TMB was increased. Receiver operating characteristic analysis demonstrated that, for correct classification, the cut-point for each gene panel may vary more than 20%. In conclusion, we here demonstrate that a major limitation for the use of gene panels is inter-assay variation and the need for dynamic thresholds to compare TMB outcomes.
Memristive synapses connect brain and silicon spiking neurons
Authors: Serb Alexantrou , Corna Andrea , George Richard , Khiat Ali , Rocchi Federico , Reato Marco , Maschietto Marta , Mayr Christian , Indiveri Giacomo , Vassanelli Stefano , Prodromakis Themistoklis 
Published: February 2020

AbstractBrain function relies on circuits of spiking neurons with synapses playing the key role of merging transmission with memory storage and processing. Electronics has made important advances to emulate neurons and synapses and brain-computer interfacing concepts that interlink brain and brain-inspired devices are beginning to materialise. We report on memristive links between brain and silicon spiking neurons that emulate transmission and plasticity properties of real synapses. A memristor paired with a metal-thin film titanium oxide microelectrode connects a silicon neuron to a neuron of the rat hippocampus. Memristive plasticity accounts for modulation of connection strength, while transmission is mediated by weighted stimuli through the thin film oxide leading to responses that resemble excitatory postsynaptic potentials. The reverse brain-to-silicon link is established through a microelectrode-memristor pair. On these bases, we demonstrate a three-neuron brain-silicon network where memristive synapses undergo long-term potentiation or depression driven by neuronal firing rates.
Tracking Gold Nanorods’ Interaction with Large 3D Pancreatic-Stromal Tumor Spheroids by Multimodal Imaging: Fluorescence, Photoacoustic, and Photothermal Microscopies
Authors: Darrigues Emilie , Nima Zeid A. , Nedosekin Dmitry A. , Watanabe Fumiya , Alghazali Karrer M. , Zharov Vladimir P. , Biris Alexandru S. 
Published: February 2020

AbstractPancreatic cancer is one of the most complex types of cancers to detect, diagnose, and treat. However, the field of nanomedicine has strong potential to address such challenges. When evaluating the diffusion and penetration of theranostic nanoparticles, the extracellular matrix (ECM) is of crucial importance because it acts as a barrier to the tumor microenvironment. In the present study, the penetration of functionalized, fluorescent gold nanorods into large (>500 μm) multicellular 3D tissue spheroids was studied using a multimodal imaging approach. The spheroids were generated by co-culturing pancreatic cancer cells and pancreatic stellate cells in multiple ratios to mimic variable tumor-stromal compositions and to investigate nanoparticle penetration. Fluorescence live imaging, photothermal, and photoacoustic analysis were utilized to examine nanoparticle behavior in the spheroids. Uniquely, the nanorods are intrinsically photoacoustic and photothermal, enabling multi-imaging detection even when fluorescence tracking is not possible or ideal.
Mandibular Advancement Devices Prevent the Adverse Cardiac Effects of Obstructive Sleep Apnea-Hypopnea Syndrome (OSAHS)
Authors: Liu Chunyan , Kang Wenjing , Zhang Shilong , Qiao Xing , Yang Xiuchun , Zhou Zheng , Lu Haiyan 
Published: February 2020

AbstractAlthough considerable research highlights the interactions between obstructive sleep apnea-hypopnea syndrome (OSAHS) and cardiovascular diseases, the effect of mandibular advancement device (MAD) treatment on cardiovascular complications in OSAHS patients remains unclear. We evaluated the effect of OSAHS treatment with MADs on the myocardium. All methods in this study were in accordance with relevant guidelines and regulations of the medical ethics committee in Hospital of Stomatology, Hebei Medical University approved the work. Thirty New Zealand rabbits were randomized into three groups: the control group, Group OSAHS, and Group MAD. Hydrophilic polyacrylamide gel was injected into the soft palate of the rabbits to induce OSAHS. In Group MAD, a MAD was positioned after OSAHS induction. All animals were induced to sleep in a supine position for 4–6 h/day for 8 weeks. Echocardiography was used to determine the structure and function of the heart. The histological changes were detected by optical microscopy and transmission electron microscopy (TEM). The levels of ET-1(endothelin-1) and Ang II (Angiotensin II) in the plasma were measured by an enzyme-linked immunosorbent assay (ELISA). The expression of ET-1 mRNA in heart tissue was detected by RT-PCR. Histological abnormalities, left ventricular hypertrophy, and left ventricular dysfunctions were demonstrated in Group OSAHS, and the abnormities were rescued with MAD treatment. Higher levels of plasma ET-1 and Ang II and elevated expression of ET-1 mRNA in cardiac tissue were detected in Group OSAHS compared with Group MAD and the control group. The blood oxygen saturation was negatively correlated with the levels of ET-1 and Ang II. OSAHS-induced elevated levels of ET-1 and Ang II may be attributed to myocardial structural abnormalities and dysfunction. Early treatment of MADs may play an important role in preventing myocardial damage in OSAHS rabbit model.
Integrated transcriptomic correlation network analysis identifies COPD molecular determinants
Authors: Paci Paola , Fiscon Giulia , Conte Federica , Licursi Valerio , Morrow Jarrett , Hersh Craig , Cho Michael , Castaldi Peter , Glass Kimberly , Silverman Edwin K. , Farina Lorenzo 
Published: February 2020

AbstractChronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called “switch genes” - for the disease. Genes contributing to common biological processes or defining given cell types are usually co-regulated and co-expressed, forming expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.
Multiple Facets of Value-Based Decision Making in Major Depressive Disorder
Authors: Mukherjee Dahlia , Lee Sangil , Kazinka Rebecca , D. Satterthwaite Theodore , Kable Joseph W. 
Published: February 2020

AbstractDepression is clinically characterized by obvious changes in decision making that cause distress and impairment. Though several studies suggest impairments in depressed individuals in single tasks, there has been no systematic investigation of decision making in depression across tasks. We compare participants diagnosed with Major Depressive Disorder (MDD) (n = 64) to healthy controls (n = 64) using a comprehensive battery of nine value-based decision-making tasks which yield ten distinct measures. MDD participants performed worse on punishment (d = −0.54) and reward learning tasks (d = 0.38), expressed more pessimistic predictions regarding winning money in the study (d = −0.47) and were less willing to wait in a persistence task (d = −0.39). Performance on learning, expectation, and persistence tasks each loaded on unique dimensions in a factor analysis and punishment learning and future expectations each accounted for unique variance in predicting depressed status. Decision-making performance alone could predict depressed status out-of-sample with 72% accuracy. The findings are limited to MDD patients ranging between moderate to severe depression and the effects of medication could not be accounted for due to the cross sectional nature of the study design. These results confirm hints from single task studies that depression has the strongest effects on reinforcement learning and expectations about the future. Our results highlight the decision processes that are impacted in major depression, and whose further study could lead to a more detailed computational understanding of distinct facets of this heterogeneous disorder.
Novel pathogenic alterations in pediatric and adult desmoid-type fibromatosis – A systematic analysis of 204 cases
Authors: Trautmann Marcel , Rehkämper Jan , Gevensleben Heidrun , Becker Jessica , Wardelmann Eva , Hartmann Wolfgang , Grünewald Inga , Huss Sebastian 
Published: February 2020

AbstractDesmoid-type fibromatosis (DTF, aggressive fibromatosis) is a non-metastasizing mesenchymal neoplasm of deep soft tissue with a tendency towards local recurrence. Genetic alterations affecting canonical Wnt/β-catenin signaling are reported in the majority of DTF. While most sporadic DTF harbor somatic mutations in CTNNB1, germline mutations in adenomatous polyposis coli (APC) are known to occur in hereditary DTF types (FAP, Gardner-Syndrome). Additional single nucleotide variants (SNVs) in AKT1 (E17K) and BRAF (V600E) were reported in pediatric DTF with potential clinical implications. We performed targeted next-generation sequencing (NGS) in a large cohort of 204 formalin-fixed DTF samples, comprising 22 pediatric cases (patients age ≤18 years). The mutational status was correlated with clinicopathological characteristics. Overall, deleterious CTNNB1 mutations were detected in 89% of DTF, most frequently affecting the serine/threonine phosphorylation sites T41 and S45 of β-catenin. While the T41A CTNNB1 mutation was significantly more often identified in the mesenterial localization, DTF originating from extra-intestinal sites more frequently harbored the S45P CTNNB1 alteration. Beyond common mutations in CTNNB1, additional SNVs were demonstrated in 7% of the DTF cohort and in 18% of the pediatric DTF subgroup. The mutational spectrum included deleterious mutations in AKT1 (G311S/D and T312I), ALK (R806H and G924S), AR (A159T), EGFR (P848L), ERBB2 (H174Y), IDH2 (H354Y), KIT (V559D), RET (T1038A), SDHA (R325M), and SDHD (R115W), as characterized by in silico prediction tools. In conclusion, our study indicates that DTF may harbor a broader mutational spectrum beyond CTNNB1 mutations, comprising targetable alterations including the herewith first reported imatinib-sensitive KIT V559D mutation in DTF.
Identification of a novel trigger complex that facilitates ribosome-associated quality control in mammalian cells
Authors: Hashimoto Satoshi , Sugiyama Takato , Yamazaki Reina , Nobuta Risa , Inada Toshifumi 
Published: February 2020

AbstractRibosome stalling triggers the ribosome-associated quality control (RQC) pathway, which targets collided ribosomes and leads to subunit dissociation, followed by proteasomal degradation of the nascent peptide. In yeast, RQC is triggered by Hel2-dependent ubiquitination of uS10, followed by subunit dissociation mediated by the RQC-trigger (RQT) complex. In mammals, ZNF598-dependent ubiquitination of collided ribosomes is required for RQC, and activating signal cointegrator 3 (ASCC3), a component of the ASCC complex, facilitates RQC. However, the roles of other components and associated factors of the ASCC complex remain unknown. Here, we demonstrate that the human RQC-trigger (hRQT) complex, an ortholog of the yeast RQT complex, plays crucial roles in RQC. The hRQT complex is composed of ASCC3, ASCC2, and TRIP4, which are orthologs of the RNA helicase Slh1(Rqt2), ubiquitin-binding protein Cue3(Rqt3), and zinc-finger type protein yKR023W(Rqt4), respectively. The ATPase activity of ASCC3 and the ubiquitin-binding activity of ASCC2 are crucial for triggering RQC. Given the proposed function of the RQT complex in yeast, we propose that the hRQT complex recognizes the ubiquitinated stalled ribosome and induces subunit dissociation to facilitate RQC.
The Prognostic Implications of Tumor Infiltrating Lymphocytes in Colorectal Cancer: A Systematic Review and Meta-Analysis
Authors: Idos Gregory E. , Kwok Janet , Bonthala Nirupama , Kysh Lynn , Gruber Stephen B. , Qu Chenxu 
Published: February 2020

AbstractTumor-infiltrating lymphocytes (TILs) are an important histopathologic feature of colorectal cancer that confer prognostic information. Previous clinical and epidemiologic studies have found that the presence and quantification of tumor-infiltrating lymphocytes are significantly associated with disease-specific and overall survival in colorectal cancer. We performed a systematic review and meta-analysis, establishing pooled estimates for survival outcomes based on the presence of TILs in colon cancer. PubMed (Medline), Embase, Cochrane Library, Web of Science, and ClinicalTrials.gov were searched from inception to April 2017. Studies were included, in which the prognostic significance of intratumoral tumor infiltrating lymphocytes, as well as subsets of CD3, CD8, FOXP3, CD45R0 lymphocytes, were determined within the solid tumor center, the invasive margin, and tumor stroma. Random-effects models were calculated to estimated summary effects using hazard ratios. Forty-three relevant studies describing 21,015 patients were included in our meta-analysis. The results demonstrate that high levels of generalized TILS as compared to low levels had an improved overall survival (OS) with a HR of 0.65 (p = <0.01). In addition, histologically localized CD3+ T-cells at the tumor center were significantly associated with better disease-free survival (HR = 0.46, 95% CI 0.36–0.61, p = 0.05), and CD3 + cells at the invasive margin were associated with improved disease-free survival (HR = 0.57, 95% CI 0.38–0.86, p = 0.05). CD8+ T-cells at the tumor center had statistically significant prognostic value on cancer-specific survival and overall survival with HRs of 0.65 (p = 0.02) and 0.71 (p < 0.01), respectively. Lastly, FOXP3+ T-cells at the tumor center were associated with improved prognosis for cancer-specific survival (HR = 0.65, p < 0.01) and overall survival (HR = 0.70, p < 0.01). These findings suggest that TILs and specific TIL subsets serve as prognostic biomarkers for colorectal cancer.
Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling
Authors: Fidler Gabor , Tolnai Emese , Stagel Aniko , Remenyik Judit , Stundl Laszlo , Gal Ferenc , Biro Sandor , Paholcsek Melinda 
Published: February 2020

AbstractHere, we developed protocols to improve sensitivity, rigor and comparability of 16S rRNA gene amplification-based next-generation sequencing (NGS) results. A thorough study was performed by evaluating extraction efficiency with respect to the yield, purity, fragmentation of the purified DNA, and sequencing metrics considering the number of quality reads, amplicon sequence variants (ASVs), community structure and biodiversity. We identified batch-effects that significantly bias broiler gastrointestinal tract (GIT) community compositions and made recommendations to improve sensitivity, consistency, and cross-study comparability. We found that the purity of the extracted nucleic acid had a strong effect on the success rate of downstream library preparations. The preparation of stool bacterial suspensions from feces showed a significant positive influence on community biodiversity by enriching Gram-negative bacteria and cataloguing low abundant taxa with greater success than direct processing of fecal material. Applications relying on the automated Roche MagNa Pure 24 magnetic-bead based method provided results with high consistency therefore it seems to be the optimal choice in large-scale studies for investigating broiler GIT microbiota.
A predominant involvement of the triple seropositive patients and others with rheumatoid factor in the association of smoking with rheumatoid arthritis
Authors: Regueiro Cristina , Rodriguez-Rodriguez Luis , Lopez-Mejias Raquel , Nuño Laura , Triguero-Martinez Ana , Perez-Pampin Eva , Corrales Alfonso , Villalba Alejandro , Lopez-Golan Yolanda , Abasolo Lydia , Remuzgo-Martínez Sara , Ortiz Ana M. , Herranz Eva , Martínez-Feito Ana , Conde Carmen , Mera-Varela Antonio , Balsa Alejandro , Gonzalez-Alvaro Isidoro , González-Gay Miguel Ángel , Fernandez-Gutierrez Benjamín , Gonzalez Antonio 
Published: February 2020

AbstractThe major environmental risk factor for rheumatoid arthritis (RA) is smoking, which according to a widely accepted model induces protein citrullination in the lungs, triggering the production of anti-citrullinated protein antibodies (ACPA) and RA development. Nevertheless, some research findings do not fit this model. Therefore, we obtained six independent cohorts with 2253 RA patients for a detailed analysis of the association between smoking and RA autoantibodies. Our results showed a predominant association of smoking with the concurrent presence of the three antibodies: rheumatoid factor (RF), ACPA and anti-carbamylated protein antibodies (ACarPA) (3 Ab vs. 0 Ab: OR = 1.99, p = 2.5 × 10–8). Meta-analysis with previous data (4491 patients) confirmed the predominant association with the concurrent presence of the three antibodies (3 Ab vs. 0 Ab: OR = 2.00, p = 4.4 ×10–16) and revealed that smoking was exclusively associated with the presence of RF in patients with one or two antibodies (RF+1+2vs. RF−0+1+2: OR = 1.32, p = 0.0002). In contrast, no specific association with ACPA or ACarPA was found. Therefore, these results showed the need to understand how smoking favors the concordance of RA specific antibodies and RF triggering, perhaps involving smoking-induced epitope spreading and other hypothesized mechanisms.
Serum Activin A Levels and Renal Outcomes After Coronary Angiography
Authors: Tsai Yi-Lin , Chou Ruey-Hsing , Lu Ya-Wen , Liu Chung-te , Huang Po-Hsun , Lin Shing-Jong 
Published: February 2020

AbstractPrevention for contrast-induced nephropathy (CIN) is limited by the lack of a single predictor. As activin A is upregulated in heart failure and chronic kidney disease, we aimed to clarify the association between activin A levels and renal outcomes after coronary angiography (CAG). This prospective observational study included 267 patients who received CAG between 2009 and 2015. CIN was defined as elevation of serum creatinine to >0.5 mg/dL or to >25% above baseline within 48 hours after CAG. During follow-up, laboratory parameters were measured every 3–6 months. Renal decline was defined as>2-fold increase in serum creatinine or initiation of dialysis. The patients were stratified into tertiles according to serum activin A levels at baseline. High activin A tertile was significantly associated more CIN and renal function decline compared to low activin A tertile (all p < 0.001). After adjusting potential confounding factors, high serum activin A tertiles was associated to CIN (Odds ratio 4.49, 95% CI 1.07–18.86, p = 0.040) and renal function decline (Hazard ratio 4.49, 95% CI 1.27–11.41, p = 0.017) after CAG.