bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pollen derived macromolecules serve as a new class of ice-nucleating cryoprotectants
Authors: Murray Kathryn A. , Kinney Nina L. H. , Griffiths Christopher A. , Hasan Muhammad , Gibson Matthew I. , Whale Thomas F. 
Published: July 2022

AbstractCryopreservation of biological material is vital for existing and emerging biomedical and biotechnological research and related applications, but there remain significant challenges. Cryopreservation of cells in sub-milliliter volumes is difficult because they tend to deeply supercool, favoring lethal intracellular ice formation. Some tree pollens are known to produce polysaccharides capable of nucleating ice at warm sub-zero temperatures. Here we demonstrated that aqueous extractions from European hornbeam pollen (pollen washing water, PWW) increased ice nucleation temperatures in 96-well plates from ≈ − 13 °C to ≈ − 7 °C. Application of PWW to the cryopreservation of immortalized T-cells in 96-well plates resulted in an increase of post-thaw metabolic activity from 63.9% (95% CI [58.5 to 69.2%]) to 97.4% (95% CI [86.5 to 108.2%]) of unfrozen control. When applied to cryopreservation of immortalized lung carcinoma monolayers, PWW dramatically increased post-thaw metabolic activity, from 1.6% (95% CI [− 6.6 to 9.79%]) to 55.0% (95% CI [41.6 to 68.4%]). In contrast to other ice nucleating agents, PWW is soluble, sterile and has low cytotoxicity meaning it can be readily incorporated into existing cryopreservation procedures. As such, it can be regarded as a unique class of cryoprotectant which acts by inducing ice nucleation at warm temperatures.
Un-biased housekeeping gene panel selection for high-validity gene expression analysis
Authors: Casas Ana I. , Hassan Ahmed A. , Manz Quirin , Wiwie Christian , Kleikers Pamela , Egea Javier , López Manuela G. , List Markus , Baumbach Jan , Schmidt Harald H. H. W. 
Published: July 2022

AbstractDifferential gene expression normalised to a single housekeeping (HK) is used to identify disease mechanisms and therapeutic targets. HK gene selection is often arbitrary, potentially introducing systematic error and discordant results. Here we examine these risks in a disease model of brain hypoxia. We first identified the eight most frequently used HK genes through a systematic review. However, we observe that in both ex-vivo and in vivo, their expression levels varied considerably between conditions. When applying these genes to normalise expression levels of the validated stroke target gene, inducible Nox4, we obtained opposing results. As an alternative tool for unbiased HK gene selection, software tools exist but are limited to individual datasets lacking genome-wide search capability and user-friendly interfaces. We, therefore, developed the HouseKeepR algorithm to rapidly analyse multiple gene expression datasets in a disease-specific manner and rank HK gene candidates according to stability in an unbiased manner. Using a panel of de novo top-ranked HK genes for brain hypoxia, but not single genes, Nox4 induction was consistently reproduced. Thus, differential gene expression analysis is best normalised against a HK gene panel selected in an unbiased manner. HouseKeepR is the first user-friendly, bias-free, and broadly applicable tool to automatically propose suitable HK genes in a tissue- and disease-dependent manner.
A hackable, multi-functional, and modular extrusion 3D printer for soft materials
Authors: Lei Iek Man , Sheng Yaqi , Lei Chon Lok , Leow Cillian , Huang Yan Yan Shery 
Published: July 2022

AbstractThree-dimensional (3D) printing has emerged as a powerful tool for material, food, and life science research and development, where the technology’s democratization necessitates the advancement of open-source platforms. Herein, we developed a hackable, multi-functional, and modular extrusion 3D printer for soft materials, nicknamed Printer.HM. Multi-printhead modules are established based on a robotic arm for heterogeneous construct creation, where ink printability can be tuned by accessories such as heating and UV modules. Software associated with Printer.HM were designed to accept geometry inputs including computer-aided design models, coordinates, equations, and pictures, to create prints of distinct characteristics. Printer.HM could further perform versatile operations, such as liquid dispensing, non-planar printing, and pick-and-place of meso-objects. By ‘mix-and-match’ software and hardware settings, Printer.HM demonstrated printing of pH-responsive soft actuators, plant-based functional hydrogels, and organ macro-anatomical models. Integrating affordability and open design, Printer.HM is envisaged to democratize 3D printing for soft, biological, and sustainable material architectures.
Relationship of lower limb geometrics with femorotibial osteoarthritis in the toei cohort
Authors: Tran Dung Huu , Hoshino Hironobu , Matsuyama Yukihiro 
Published: July 2022

AbstractOsteoarthritis (OA) is a common disease of joints that is more common in females than in males. It is characterized by severe knee degeneration, damaged cartilage and appearance of osteophytes. Hip geometry and morphometric parameters in the knee joint vary between the sexes and depend on the severity of OA and the presence of osteophytes. Very few studies have assessed this phenomenon; therefore in this study, we assessed the difference in hip geometry and morphometric parameters in the lower limbs of males and females and evaluated the association of the differences with the presence or absence of osteophytes. Three hundred and six knees volunteers (104 male knees and 202 female knees) from the Toei region were included in the study between 2012 and 2018. The parameters measured were from the anteroposterior and lateral views of the hip and anteroposterior view of the knee. The participants were divided into 4 groups based on the assessment for osteophytes: Group 1 had no osteophytes, Group 2 had lateral compartment osteophytes, Group 3 had medial compartment osteophytes, and Group 4 had osteophytes in both compartments. Males had an increased femoral neck-shaft angle, femoral-tibial angle, and plateau angle, and a decreased femoral offset, femoral neck length, fibular-tibial angle, and knee rotation index than females. Group 2 had a greater height of the hip center, the angle between the femoral mechanical axis and the femoral shaft axis, condylar-hip angle, and plateau angle than Group 1. Group 3 showed an increased abductor angle, the angle between the femoral mechanical axis and the femoral shaft axis. Group 4 showed an increased angle between the femoral mechanical axis and the femoral shaft axis, femoral-tibial angle, and a decreased patellar shift index and knee rotation index. The angle between the femoral mechanical axis and the femoral shaft axis, condylar-hip angle, femoral-tibial angle, plateau angle, patellar shift index, and knee rotation index were different in both sexes and may be dependent on the presence or absence of osteophytes.
Eosinophilic esophagitis auxiliary diagnosis based on a peptide ligand to eosinophil cationic protein in esophageal mucus of pediatric patients
Authors: de Souza Tafarel Andrade , Carneiro Ana Paula , Narciso Andreia S. , Barros Cristina P. , Alves Douglas Alexsander , Marson Luciane B. , Tunala Tatiane , de Alcântara Tânia M. , de Paiva Maia Yara Cristina , Briza Peter , Ferreira Fatima , Goulart Luiz R. 
Published: July 2022

AbstractEosinophilic esophagitis (EoE) is a chronic inflammatory condition of the esophagus characterized by increased number of eosinophils. Currently, EoE diagnosis is based on endoscopic procedures for histopathological examination, eosinophils’ counting and, often, in clinical practice, the challenge is the differentiation between EoE and gastroesophageal reflux disease (GERD). Our aim was to develop novel peptide ligand to Eosinophil cationic protein (ECP) present in EoE biopsies of patients with potential to be used for detection. We performed a comparative proteomic analysis using liquid chromatography-tandem mass spectrometry (LC–MS/MS) of esophageal biopsies from pediatric patients with eosinophilic esophagitis, gastroesophageal reflux disease and control individuals. Then, phage display technology was used to select peptides against specific up-regulated protein from EoE patients. Twelve phage clones were selected after three biopanning rounds, and the best phage clone reactivity was evaluated by phage-ELISA assay using esophageal mucus samples from 94 pediatric patients. Mass spectrometry showed that eosinophil cationic protein (ECP) was one of the most up-regulated proteins in EoE patients, which is an eosinophil granule protein usually deposited on tissues to mediate remodeling, but in excess may cause fibrosis and hypertrophy, especially in allergic responses. A highly reactive ECP-ligand peptide (E5) was able to distinguish reactive mucus of EoE patients from GERD and the control individuals by Phage-ELISA, achieving a sensitivity of 84.62%, and a specificity of 82.72%. This is the first study that successfully demonstrated an antibody-like peptide targeting ECP at the esophagus mucus as a useful auxilliary tool for EoE diagnosis with a significant association with atopic disorders and dysphagia.ClinicalTrials.gov no.: NCT03069573.
Machine learning approach towards explaining water quality dynamics in an urbanised river
Authors: Schäfer Benjamin , Beck Christian , Rhys Hefin , Soteriou Helena , Jennings Paul , Beechey Allen , Heppell Catherine M. 
Published: July 2022

AbstractHuman activities alter river water quality and quantity, with consequences for the ecosystems of urbanised rivers. Quantifying the role of human-induced drivers in controlling spatio-temporal patterns in water quality is critical to develop successful strategies for improving the ecological health of urban rivers. Here, we analyse high-frequency electrical conductivity and temperature data collected from the River Chess in South-East England during a Citizen Science project. Utilizing machine learning, we find that boosted trees outperform GAM and accurately describe water quality dynamics with less than 1% error. SHapley Additive exPlanations reveal the importance of and the (inter)dependencies between the individual variables, such as river level and Wastewater Treatment Works (WWTW) outflow. WWTW outflows give rise to diurnal variations in electrical conductivity, which are detectable throughout the year, and to an increase in average water temperature of 1 $$\rm{^o}C$$

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in a 2 km reach downstream of the wastewater treatment works during low flows. Overall, we showcase how high-frequency water quality measurements initiated by a Citizen Science project, together with machine learning techniques, can help untangle key drivers of water quality dynamics in an urbanised chalk stream.
Three and two-dimensional cardiac mechanics by speckle tracking are predictors of outcomes in chagas heart disease
Authors: Hotta Viviane Tiemi , Abduch Maria Cristina Donadio , Vieira Marcelo Luiz Campos , de Andrade Vilela Andrea , Bocchi Edimar Alcides 
Published: July 2022

AbstractChagas disease (CD) is a neglected infectious disease associated with early mortality and substantial disability. Three-dimensional speckle tracking (3D STE) may play a role in the evaluation of CD. We aim to characterize new echocardiographic variables in patients with CD and to assess the hypothesis that 3D STE may predict outcomes. Seventy-two patients with CD were included. Clinical and conventional 2D and 3D STE analysis were performed. Patients were followed up for 60 months. Clinical events were defined as hospitalization for heart failure, complex ventricular arrhythmias, heart transplant and all-cause death. Seventy-two patients were recruited and enrolled in three groups: left ventricular ejection fraction (LVEF) < 0.40 (N = 22; reduced LVEF or rLVEF); 0.40 ≤ LVEF ≤ 0.50 (N = 10; mildly reduced LVEF or mrLVEF) and LVEF > 0.50 (N = 30; preserved LVEF or pLVEF). After a Cox model analysis, the top predictors of composite endpoints were 2D LV global longitudinal strain (GLS) ≤ − 11.3% (AUC = 0.87), 2D LV global circumferential strain (GCS) ≤  − 10.1% (AUC = 0.79), 3D LV GLS ≤ − 13% (AUC = 0.82), 3D LV area strain ≤ − 16% (AUC = 0.81) and right ventricle (RV) GLS ≤ − 17.2% (AUC = 0.78). Patients with CD and mrLVEF were morphologically similar to the rLVEF patients despite the benign evolution as the pLVEF group. RV GLS, 2D LV GLS, 2D LV GCS, 3D LV GLS, and 3D LV area strain are strong predictors of 60 months outcomes in patients with CD.
Inhibition of cell invasion and migration by targeting matrix metalloproteinase-9 expression via sirtuin 6 silencing in human breast cancer cells
Authors: Hong On-Yu , Jang Hye-Yeon , Lee Young-Rae , Jung Sung Hoo , Youn Hyun Jo , Kim Jong-Suk 
Published: July 2022

AbstractSirtuin 6 (SIRT6) regulation is involved in carcinogenesis. However, its role in breast cancer (BC) metastasis remains unclear. We investigated the effects of SIRT6 on protein kinase C activator- and cytokine-mediated cancer cell invasion and migration in MCF-7 and MDA-MB-231 cells and the association between SIRT6 and matrix metalloproteinase-9 (MMP-9) expression. To assess MMP-9 and SIRT6 expression in patients, protein levels in BC tissues were analyzed. MCF-7 and MDA-MB-231 cell viability was analyzed using MTT assays. SIRT6 was silenced in both cell lines and protein secretion, expression, and mRNA levels were analyzed. Transcription factor DNA activity was investigated using luciferase assays. Matrigel invasion assays were used to assess the effects of SIRT6 in both cell lines. SIRT6 and MMP-9 expression in cancer tissues was significantly higher than in paired normal breast tissues. 12-O-tetradecanoylphorbol-13-acetate (TPA) or tumor necrosis factor-α (TNF-α) increased MMP-9 expression and cell invasion and migration, but SIRT6 knockdown abolished these effects. SIRT6 overexpression additively increased TPA- and TNF-α-induced MMP-9 expression. SIRT6 knockdown suppressed the mitogen-activated protein kinase (MAPK) signaling pathway and thus TPA- and TNF-α-induced MMP-9 expression. SIRT6 silencing suppressed TPA- and TNF-α-induced nuclear factor-κB (NF-κB) and activator protein-1 (AP-1) expressions in both cell lines, and treatment with MAPK, NF-κB, and AP-1 inhibitors reduced MMP-9 expression. The anti-invasive effects of SIRT6 in BC cells might be mediated by suppression of MAPK phosphorylation and reduction in NF-κB and AP-1 DNA activities, leading to MMP-9 downregulation, suggesting that SIRT6 modulation has the potential to target BC metastasis.
Low frequency visual stimulation enhances slow wave activity without disrupting the sleep pattern in mice
Authors: Thankachan Stephen , Yang Chun , Kastanenka Ksenia V. , Bacskai Brian J. , Gerashchenko Dmitry 
Published: July 2022

AbstractNon-invasive stimulation technologies are emerging as potential treatment options for a range of neurodegenerative disorders. Experimental evidence suggests that stimuli-evoked changes in slow brain rhythms may mitigate or even prevent neuropathological and behavioral impairments. Slow wave activity is prevalent during sleep and can be triggered non-invasively by sensory stimulation targeting the visual system or directly via activation of neurons locally using optogenetics. Here, we developed new tools for delivering visual stimulation using light-emitting diodes in freely moving mice while awake and during sleep. We compared these tools to traditional optogenetic approaches used for local stimulation of neurons in the cerebral cortex. We then used these tools to compare the effects of low-frequency visual versus optogenetic stimulations on the slow wave activity and sleep pattern in mice. Visual stimulation effectively enhanced slow wave activity without disrupting the sleep pattern. Optogenetic stimulation of cortical GABAergic neurons increased NREM sleep. These results suggest that visual stimulation can be effective at boosting slow wave activity without having adverse effects on sleep and thus holds great potential as a non-invasive stimulation treatment strategy.
A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants
Authors: Hussain Athar , Liu Jinbao , Mohan Binoop , Burhan Akif , Nasim Zunaira , Bano Raveena , Ameen Ayesha , Zaynab Madiha , Mukhtar M. Shahid , Pajerowska-Mukhtar Karolina M. 
Published: July 2022

AbstractZinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs inGossypiumsp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species.
Exploration of two-dimensional molybdenum-borides and potential applications
Authors: Jin Junjie , Schwingenschlögl Udo 
Published: July 2022

AbstractThe recent discovery of MBenes has generated interest in two-dimensional metal-borides, which are expected to show rich electrochemical properties. Using evolutionary search combined with ab initio calculations, we discover that the MoBx (x = 1, 3, and 4) monolayers, two-dimensional metal-borides, are dynamically, mechanically, and thermally stable. Due to their metallic characters, we investigate the potential of application as anode materials of Li-ion batteries. The MoB and MoB3 monolayers are found to provide excellent properties, combining high Li-specific capacities of 670 and 418 mA h g−1 with low Li diffusion barriers of 0.10 and 0.13 eV, respectively.
Blood‐contaminated endoscopic image restoration based on residual VQ‐VAE with cascaded structure
Authors: Lin Jie , Pan Yulong , Dang Yuan , Bao Yige , Zhuo Hui 
Published: July 2022

AbstractThis research studies an image reconstruction technology that can help doctors observe endoscopic images obscured by blood in transurethral procedures. A new network structure is proposed, which applies encoder–decoder deep neural network to achieve the purpose of denoising and uses residual learning and cascade learning methods to relieve the problem of insufficient clarity and lack of detail in reconstruction image when restoring endoscopic images suffered from blood occlusion. The residual mechanism is used to estimate noise and compensate the images, instead of reconstructing overall image by an encoder and decoder deep network. It can potentially make the details of the image to be preserved and improve the resolution of the reconstructed image. This denoising model is embedded into a cascade network framework to further improve the quality of the restored image through the idea of repeated learning multiple times. On a customized endoscopic image sample set with real blood noise, for verifying the denoising ability, we designed two approaches of data augmentation to generate noised images obscured by different types and degree blood noises. In experiments, the new model has been compared to other approaches and the certain improved denoising effects can be observed.
A Comparative Study of Urinary Complication Rates before and after the Incorporation of a Urethral Lengthening Technique during Masculinizing Genital Gender Affirmation Surgery
Authors: Gupta Richie , Gupta Rajat , Puri Anurag 
Published: July 2022

Abstract
Objectives Masculinizing genital gender affirmation surgery (MgGAS) consists of operative procedures designed to help the transition of transmen in their journey toward male gender role. Phalloplasty and urethral lengthening remain the most challenging of these surgeries, as the female urethra (4 cm long) must be lengthened to male dimensions (15–29 cm) with anastomosis at two sites, the native urethra/pars fixa urethra and the pars fixa urethra-penile urethra. As a result, there is a high incidence of urinary complications such as strictures and fistulae. Authors incorporated a urethral lengthening technique to reduce urinary complications in MgGAS. They compare the rates of urinary complications rates in cohorts before and after the introduction of this technique.
Materials and Methods Authors have been performing phalloplasty since past 27 years, utilizing mainly free radial artery forearm flap (fRAFFp 431 cases) and pedicled anterolateral thigh flap (pALTp 120 cases). A retrospective review and comparison of urinary complications were performed before and after the introduction of their new technique since March 2017.
Results There was a statistically significant reduction in the incidence of stricture with and without fistulae (25.94% with conventional and 4.17% with urethral lengthening technique p = 0.001) and fistulae alone (12.81% with conventional and 2.78% with urethral lengthening technique p = 0.011) in fRAFFp cases. In pALTp cases, the respective reductions were 43.08 to 17.07%, p = 0.006 (significant), and 13.85 to 4.88%, p = 0.197 (not statistically significant).
Conclusion Over years, the rates of urinary complications in MgGAS have remained constant, varying from 25 to 58% for strictures and 17 to 75% for fistulae as noted by many authors. Authors noted that in most of their cases, strictures occurred at distal pars fixa urethra (DPFU)-penile urethra anastomosis and incorporated a urethral lengthening technique, which lengthens the DPFU by 3 to 5 cm at this anastomotic site, thus significantly reducing the anastomotic tension and the rate of urinary complications.