bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of salt stress in wheat leaves by Raman spectroscopy and machine learning
Authors: Kecoglu Ibrahim , Sirkeci Merve , Unlu Mehmet Burcin , Sen Ayse , Parlatan Ugur , Guzelcimen Feyza 
Published: May 2022

AbstractThe salinity level of the growing medium has diverse effects on the development of plants, including both physical and biochemical changes. To determine the salt stress level of a plant endures, one can measure these structural and chemical changes. Raman spectroscopy and biochemical analysis are some of the most common techniques in the literature. Here, we present a combination of machine learning and Raman spectroscopy with which we can both find out the biochemical change that occurs while the medium salt concentration changes and predict the level of salt stress a wheat sample experiences accurately using our trained regression models. In addition, by applying different machine learning algorithms, we compare the level of success for different algorithms and determine the best method to use in this application. Production units can take actions based on the quantitative information they get from the trained machine learning models related to salt stress, which can potentially increase efficiency and avoid the loss of crops.
Spatiotemporal neural network with attention mechanism for El Niño forecasts
Authors: Kim Jinah , Kwon Minho , Kim Sung-Dae , Kug Jong-Seong , Ryu Joon-Gyu , Kim Jaeil 
Published: May 2022

AbstractTo learn spatiotemporal representations and anomaly predictions from geophysical data, we propose STANet, a spatiotemporal neural network with a trainable attention mechanism, and apply it to El Niño predictions for long-lead forecasts. The STANet makes two critical architectural improvements: it learns spatial features globally by expanding the network’s receptive field and encodes long-term sequential features with visual attention using a stateful long-short term memory network. The STANet conducts multitask learning of Nino3.4 index prediction and calendar month classification for predicted indices. In a comparison of the proposed STANet performance with the state-of-the-art model, the accuracy of the 12-month forecast lead correlation coefficient was improved by 5.8% and 13% for Nino3.4 index prediction and corresponding temporal classification, respectively. Furthermore, the spatially attentive regions for the strong El Niño events displayed spatial relationships consistent with the revealed precursor for El Niño occurrence, indicating that the proposed STANet provides good understanding of the spatiotemporal behavior of global sea surface temperature and oceanic heat content for El Niño evolution.
Dynamics of parasympathetic activity in violent incarcerated offenders before, during, and in recovery from an emotional inhibition task
Authors: Palix Julie , Gillespie Steven M. , Abbiati Milena , Abu-Akel Ahmad 
Published: May 2022

AbstractDynamics of the autonomic nervous system (ANS) are hypothesized to play a role in the emergence of interpersonal violence. In the present study, we examined continuous activities of the inhibitory parasympathetic pathway of the ANS through the root mean square of successive differences between normal heartbeats (RMSSD) in 22 male offenders who committed interpersonal violence and 24 matched controls from the general population across three successive phases: resting baseline, while performing an emotional Go/No-Go task, and post-task recovery. Results showed that across the three phases, the offender group presented lower RMSSD at baseline (pFDR = .003; Cohen’s d =  − 1.11), but similar levels during the task, attributed to a significant increase in their RMSSD level (pFDR = .027, Cohen’s d =  − 1.26). During recovery, while no distinction between the two groups was found, both groups showed signs of recovering toward baseline values. These findings suggest that violent incarcerated offenders can flexibly engage parasympathetic resources to meet environmental challenges. This underscores the necessity of considering parasympathetic dynamics and its respective mobilization/flexibility to better understand ANS profiles underlying interpersonal violence as well as its potential utility in designing more tailored interventions.
Clinical prediction model of pathological response following neoadjuvant chemoradiotherapy for rectal cancer
Authors: Shin Jung Kyong , Huh Jung Wook , Lee Woo Yong , Yun Seong Hyeon , Kim Hee Cheol , Cho Yong Beom , Park Yoon Ah 
Published: May 2022

AbstractPatients with pathologic complete response (pCR) achievement can consider local excision or “watch and wait” strategy instead of a radical surgery. This study analyzed the predictive factors of pCR in rectal cancer patients who underwent radical operation after neoadjuvant chemoradiotherapy (nCRT). This study also analyzed the recurrence patterns in patients who achieved pCR and the oncologic outcomes and prognostic factors by ypStage. Between 2000 and 2013, 1,089 consecutive rectal cancer patients who underwent radical resection after nCRT were analyzed. These patients were classified into two groups according to pCR. The clinicopathologic and oncologic outcomes were analyzed and compared between the two groups. Multivariate analysis was conducted on factors related to pCR. The proportion of patients achieving pCR was 18.2% (n = 198). The pCR group demonstrated earlier clinical T and N stages, smaller tumor size, better differentiation, and a lower percentage of circumferential resection margin (CRM) involvement than did the non-pCR group. The prognostic factors associated with poorer disease-free survival were high preoperative carcinoembryonic antigen levels, non-pCR, poor histology, lymphatic/perineural invasion, and involvement of CRM. Multivariate analysis revealed that clinical node negativity, tumor size < 4 cm, and well differentiation were significant independent clinical predictors for achieving pCR. Patients with pCR displayed better long-term outcomes than those with non-pCR. The pCR-prediction model, based on predictive factors, is potentially useful for prognosis and for prescribing a treatment strategy in patients with advanced rectal cancer who need nCRT.
Predictive value of clinical and 18F-FDG-PET/CT derived imaging parameters in patients undergoing neoadjuvant chemoradiation for esophageal squamous cell carcinoma
Authors: Marr Lisa , Haller Bernhard , Pyka Thomas , Peeken Jan C. , Jesinghaus Moritz , Scheidhauer Klemens , Friess Helmut , Combs Stephanie E. , Münch Stefan 
Published: May 2022

AbstractAim of this study was to validate the prognostic impact of clinical parameters and baseline 18F-FDG-PET/CT derived textural features to predict histopathologic response and survival in patients with esophageal squamous cell carcinoma undergoing neoadjuvant chemoradiation (nCRT) and surgery. Between 2005 and 2014, 38 ESCC were treated with nCRT and surgery. For all patients, the 18F-FDG-PET-derived parameters metabolic tumor volume (MTV), SUVmax, contrast and busyness were calculated for the primary tumor using a SUV-threshold of 3. The parameter uniformity was calculated using contrast-enhanced computed tomography. Based on histopathological response to nCRT, patients were classified as good responders (< 10% residual tumor) (R) or non-responders (≥ 10% residual tumor) (NR). Regression analyses were used to analyse the association of clinical parameters and imaging parameters with treatment response and overall survival (OS). Good response to nCRT was seen in 27 patients (71.1%) and non-response was seen in 11 patients (28.9%). Grading was the only parameter predicting response to nCRT (Odds Ratio (OR) = 0.188, 95% CI: 0.040–0.883; p = 0.034). No association with histopathologic treatment response was seen for any of the evaluated imaging parameters including SUVmax, MTV, busyness, contrast and uniformity. Using multivariate Cox-regression analysis, the heterogeneity parameters busyness (Hazard Ratio (HR) = 1.424, 95% CI: 1.044–1.943; p = 0.026) and contrast (HR = 6.678, 95% CI: 1.969–22.643;p = 0.002) were independently associated with OS, while no independent association with OS was seen for SUVmax and MTV. In patients with ESCC undergoing nCRT and surgery, baseline 18F-FDG-PET/CT derived parameters could not predict histopathologic response to nCRT. However, the PET/CT derived features busyness and contrast were independently associated with OS and should be further investigated.
A human pancreatic ECM hydrogel optimized for 3-D modeling of the islet microenvironment
Authors: Tremmel Daniel M. , Sackett Sara Dutton , Feeney Austin K. , Mitchell Samantha A. , Schaid Michael D. , Polyak Erzsebet , Chlebeck Peter J. , Gupta Sakar , Kimple Michelle E. , Fernandez Luis A. , Odorico Jon S. 
Published: May 2022

AbstractExtracellular matrix (ECM) plays a multitude of roles, including supporting cells through structural and biochemical interactions. ECM is damaged in the process of isolating human islets for clinical transplantation and basic research. A platform in which islets can be cultured in contact with natural pancreatic ECM is desirable to better understand and support islet health, and to recapitulate the native islet environment. Our study demonstrates the derivation of a practical and durable hydrogel from decellularized human pancreas that supports human islet survival and function. Islets embedded in this hydrogel show increased glucose- and KCl-stimulated insulin secretion, and improved mitochondrial function compared to islets cultured without pancreatic matrix. In extended culture, hydrogel co-culture significantly reduced levels of apoptosis compared to suspension culture and preserved controlled glucose-responsive function. Isolated islets displayed altered endocrine and non-endocrine cell arrangement compared to in situ islets; hydrogel preserved an islet architecture more similar to that observed in situ. RNA sequencing confirmed that gene expression differences between islets cultured in suspension and hydrogel largely fell within gene ontology terms related to extracellular signaling and adhesion. Natural pancreatic ECM improves the survival and physiology of isolated human islets.
Tillage, green manure and residue retention improves aggregate-associated phosphorus fractions under rice–wheat cropping
Authors: Sharma Sandeep , Kaur Sukhjinder , Parkash Choudhary Om , Singh Manpreet , Al-Huqail Asma A. , Ali Hayssam M. , Kumar Ritesh , Siddiqui Manzer H. 
Published: May 2022

AbstractThe sustainability of the rice–wheat system is threatened due to the deterioration of soil health and emergence of new challenges of climate change caused by low nutrient use efficiency and large scale burning of crop residues. The conservation agriculture based on tillage intensity, crop residue retention and raising green manuring (GM) crops during the intervening period between wheat harvest and rice establishment offers opportunities for restoration of phosphorus (P) dynamics and stimulate phosphatase activities within the macro-and micro-aggregates. Phosphorus and phosphatase activities in the soil aggregates affected by different residue management practices remain poorly understood. Thus, soil samples were obtained after a five-year field experiment to identify the effect of tillage, green manure and residue management on aggregate-associated phosphorus fractions. Four main plot treatments in rice included combination of wheat straw and GM were conventional till puddled transplanted rice (PTR) with no wheat straw (PTRW0), PTR with 25% wheat stubbles retained (PTRW25), PTR without wheat straw and GM (PTRW0 + GM), and PTR with wheat stubbles and GM (PTRW25 + GM). Three sub-plots treatments in the successive wheat crop were conventional tillage (CT) with rice straw removed (CTWR0), zero tillage (ZT) with rice straw removed (ZTWR0) and ZT with rice straw retained as surface mulch (ZTWR100). Results of the present study revealed significantly higher phosphorus fractions (HCl-P, NaHCO3-Piand NaOH-Po) in treatment PTRW25 + GM and ZTWR100compared with PTRW0/CTWR0within both macro- and micro-aggregates. The total phosphorus (P), available P, alkaline phosphatase and phytin-P were significantly higher under ZTWR100than CTWR0. The principal component analysis identified NaOH-Po, NaHCO3-Piand HCl-P as the dominant and reliable indicators for evaluating P transformation within aggregates under conservation agriculture-based practices.
Time-dependent effect of desensitization with wasp venom on selected parameters of the immune system
Authors: Szymański Łukasz , Urbańska Weronika , Ciepielak Martyna , Cios Aleksandra , Stankiewicz Wanda , Stelmasiak Marta , Rzeszotarska Agnieszka , Korsak Jolanta , Lewicki Sławomir , Chciałowski Andrzej 
Published: May 2022

AbstractThe emergence of tolerance during Hymenoptera venom immunotherapy (VIT) is a complex process. The main goal of VIT is to induce a change from proinflammatory Th2 response to the Th1 response. However, the immune mechanism of acquiring rapid tolerance during VIT has not yet been fully understood. Therefore, we have analyzed (in 4-time points: 0, 2, 6, and 24 weeks after the initiation phase of VIT) the concentration of complement C3, C4, and C5 components, lymphocyte subpopulations (flow cytometry), as well as histamine and tryptase serum concentrations of 43 patients with wasp venom allergy (III and IV Müller grade) classified to ultra-rush treatment and 18 volunteers as the control group (CG). We observed that VIT affected the immune system by inducing changes in the complement system (decreased C3 and C4 compartment protein concentrations) and "normalized" the percentage of lymphocytes and neutrophils in the peripheral blood. Moreover, a significant increase in the percentage of nTreg in the blood of patients treated with VIT was observed. On the other hand, there were no changes in histamine or tryptase concentrations in the blood. Increased percentage of nTreg cells is a well-known mechanism by which VIT affects the immune system. Finally, VIT also modulated the concentrations of the complement components, which may be a previously unknown VIT mechanism of action.
TPMS-based membrane lung with locally-modified permeabilities for optimal flow distribution
Authors: Hesselmann Felix , Halwes Michael , Bongartz Patrick , Wessling Matthias , Cornelissen Christian , Schmitz-Rode Thomas , Steinseifer Ulrich , Jansen Sebastian Victor , Arens Jutta 
Published: May 2022

AbstractMembrane lungs consist of thousands of hollow fiber membranes packed together as a bundle. The devices often suffer from complications because of non-uniform flow through the membrane bundle, including regions of both excessively high flow and stagnant flow. Here, we present a proof-of-concept design for a membrane lung containing a membrane module based on triply periodic minimal surfaces (TPMS). By warping the original TPMS geometries, the local permeability within any region of the module could be raised or lowered, allowing for the tailoring of the blood flow distribution through the device. By creating an iterative optimization scheme for determining the distribution of streamwise permeability inside a computational porous domain, the desired form of a lattice of TPMS elements was determined via simulation. This desired form was translated into a computer-aided design (CAD) model for a prototype device. The device was then produced via additive manufacturing in order to test the novel design against an industry-standard predicate device. Flow distribution was verifiably homogenized and residence time reduced, promising a more efficient performance and increased resistance to thrombosis. This work shows the promising extent to which TPMS can serve as a new building block for exchange processes in medical devices.
CRISPR-Cas9 mediated generation of a conditional poly(A) binding protein nuclear 1 (Pabpn1) mouse model reveals an essential role for hematopoietic stem cells
Authors: Sommerkamp Pia , Sommerkamp Alexander C. , Zeisberger Petra , Eiben Paula Leonie , Narr Andreas , Korkmaz Aylin , Przybylla Adriana , Sohn Markus , van der Hoeven Franciscus , Schönig Kai , Trumpp Andreas 
Published: May 2022

AbstractPoly(A) binding protein nuclear 1 (PABPN1) is known for its role in poly(A) tail addition and regulation of poly(A) tail length. In addition, it has been shown to be involved in alternative polyadenylation (APA). APA is a process regulating differential selection of polyadenylation sites, thereby influencing protein isoform expression and 3ʹ-UTR make-up. In this study, we generated an inducible Pabpn1flox/flox mouse model using crRNA-tracrRNA:Cas9 complexes targeting upstream and downstream genomic regions, respectively, in combination with a long single-stranded DNA (ssDNA) template. We performed extensive in vitro testing of various guide RNAs (gRNAs) to optimize recombination efficiency for in vivo application. Pabpn1flox/flox mice were generated and crossed to MxCre mice for validation experiments, allowing the induction of Cre expression in the bone marrow (BM) by poly(I:C) (pIC) injections. Validation experiments revealed successful deletion of Pabpn1 and absence of PABPN1 protein. Functionally, knockout (KO) of Pabpn1 led to a rapid and robust depletion of hematopoietic stem and progenitor cells (HSPCs) as well as myeloid cells, suggesting an essential role of Pabpn1 in the hematopoietic lineage. Overall, the mouse model allows an inducible in-depth in vivo analysis of the role of PABPN1 and APA regulation in different tissues and disease settings.
Mechanistic insights of ABC importer HutCD involved in heme internalization by Vibrio cholerae
Authors: Saha Indrila , Chakraborty Shrestha , Agarwal Shubhangi , Mukherjee Peeali , Ghosh Biplab , Dasgupta Jhimli 
Published: May 2022

AbstractHeme internalization by pathogenic bacteria inside a human host to accomplish the requirement of iron for important cellular processes is of paramount importance. Despite this, the mechanism of heme import by the ATP-binding-cassette (ABC) transporter HutCD inVibrio choleraeremains unexplored. We have performed biochemical studies on ATPase HutD and its mutants, along with molecular modelling, docking and unbiased all-atom MD simulations on lipid-solvated models of permease-ATPase complex HutCD. The results demonstrated mechanisms of ATP binding/hydrolysis and trapped transient and global conformational changes in HutCD, necessary for heme internalization. ATPase HutD forms a dimer, independent of the permease HutC. Each HutD monomer canonically binds ATP in a 1:1 stoichiometry. MD simulations demonstrated that a rotational motion of HutC dimer occurs synchronously with the inter-dimeric D-loop interactions of HutDs. F151 of TM4–TM5 loop of HutC, packs with ATP and Y15 of HutD, initiating ‘cytoplasmic gate opening’ which mimics an ‘outward-facing’ to ‘inward-facing’ conformational switching upon ATP hydrolysis. The simulation on ‘inward-facing’ HutCD culminates to an ‘occluded’ state. The simulation on heme-docked HutCD indicated that the event of heme release occurs in ATP-free ‘inward-facing’ state. Gradual conformational changes of the TM5 helices of HutC towards the ‘occluded’ state facilitate ejection of heme.
Between-hospital variations in 3-year survival among patients with newly diagnosed gastric, colorectal, and lung cancer
Authors: Morishima Toshitaka , Okawa Sumiyo , Koyama Shihoko , Nakata Kayo , Tabuchi Takahiro , Miyashiro Isao 
Published: May 2022

AbstractDue to increases in cancer survivability, quality assessments of cancer care must include long-term outcomes. This multicenter retrospective cohort study evaluated between-hospital variations in the 3-year survival rates of patients with gastric, colorectal, and lung cancer irrespective of treatment modality. We linked cancer registry data and administrative data from patients aged 18–99 years who were diagnosed with gastric, colorectal, or lung cancer between 2013 and 2015 in Osaka Prefecture, Japan. The 3-year survival rates were adjusted for potential prognostic factors using multilevel logistic regression models. Between-hospital variations were visually evaluated using funnel plots. We analyzed 10,296 gastric cancer patients from 30 hospitals, 9276 colorectal cancer patients from 30 hospitals, and 7978 lung cancer patients from 28 hospitals. The 3-year survival rate was 70.2%, 75.2%, and 45.0% for gastric, colorectal, and lung cancer, respectively. In the funnel plots, the adjusted survival rates of gastric and colorectal cancer for all hospitals lay between the lower and upper control limits of two standard deviations of the average survival rates. However, the adjusted survival rates of lung cancer for four hospitals lay below the lower limit while that for two hospitals lay above the upper limit. Older age, men, advanced cancer stage, comorbidities, functional disability, emergency admission, current/ex-smokers, and underweight were independently associated with poorer survival. In conclusion, there were between-hospital variations in 3-year survival for lung cancer even after adjusting for case mix. Quality improvement initiatives may be needed to raise the consistency of care.
Juvenile handling rescues autism-related effects of prenatal exposure to valproic acid
Authors: Seiffe Araceli , Ramírez Mauro Federico , Sempé Lucas , Depino Amaicha Mara 
Published: May 2022

AbstractEnvironmental factors acting on young animals affect neurodevelopmental trajectories and impact adult brain function and behavior. Psychiatric disorders may be caused or worsen by environmental factors, but early interventions can improve performance. Understanding the possible mechanisms acting upon the developing brain could help identify etiological factors of psychiatric disorders and enable advancement of effective therapies. Research has focused on the long-lasting effects of environmental factors acting during the perinatal period, therefore little is known about the impact of these factors at later ages when neurodevelopmental pathologies such as autism spectrum disorder (ASD) are usually diagnosed. Here we show that handling mice during the juvenile period can rescue a range of behavioral and cellular effects of prenatal valproic acid (VPA) exposure. VPA-exposed animals show reduced sociability and increased repetitive behaviors, along with other autism-related endophenotypes such as increased immobility in the forced swim test and increased neuronal activity in the piriform cortex (Pir). Our results demonstrate that briefly handling mice every other day between postnatal days 22 and 34 can largely rescue these phenotypes. This effect can also be observed when animals are analyzed across tests using an “autism” factor, which also discriminates between animals with high and low Pir neuron activity. Thus, we identified a juvenile developmental window when environmental factors can determine adult autism-related behavior. In addition, our results have broader implications on behavioral neuroscience, as they highlight the importance of adequate experimental design and control of behavioral experiments involving treating or testing young animals.