bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitigating sarcoplasmic reticulum stress limits disuse-induced muscle loss in hindlimb unloaded mice
Authors: Khan Amir Ali , Gul Muhammad Tehsil , Karim Asima , Ranade Anu , Azeem Muhammad , Ibrahim Zeinab , Ramachandran Gopika , Nair Vidhya A. , Ahmad Firdos , Elmoselhi Adel , Qaisar Rizwan 
Published: July 2022

AbstractMuscle disuse in the hindlimb unloaded (HU) mice causes significant atrophy and weakness. However, the cellular and molecular mechanisms driving disuse-muscle atrophy remain elusive. We investigated the potential contribution of proteins dysregulation by sarcoplasmic reticulum (SR), a condition called SR stress, to muscle loss during HU. Male, c57BL/6j mice were assigned to ground-based controls or HU groups treated with vehicle or 4-phenylbutyrate (4-PBA), a potent inhibitor of SR stress, once a day for three weeks. We report that the 4-PBA reduced the SR stress and partly reversed the muscle atrophy and weakness in the HU mice. Transcriptome analysis revealed that several genes were switched on (n = 3688) or differentially expressed (n = 1184) due to HU. GO, and KEGG term analysis revealed alterations in pathways associated with the assembly of cilia and microtubules, extracellular matrix proteins regulation, calcium homeostasis, and immune modulation during HU. The muscle restoration with 4-PBA partly reversed these changes along with differential and unique expression of several genes. The analysis of genes among the two comparisons (HU-v vs. control and HU-t vs. HU-v.) shows 841 genes were overlapped between the two comparisons and they may be regulated by 4-PBA. Altogether, our findings suggest that the pharmacological suppression of SR stress may be an effective strategy to prevent disuse-induced muscle weakness and atrophy.
Full-color-tunable phosphorescence of antimony-doped lead halide single crystal
Authors: Liao Jin-Feng , Zhang Zhipeng , Wang Bingzhe , Tang Zikang , Xing Guichuan 
Published: July 2022

AbstractAlthough multiple emissive phosphors are of great fundamental interest and practical importance, it is still challenging to achieve full-color tunable luminescence in a single-component material. Herein, we present an antimony-doped lead halide single crystal (C10NH22)2PbBr4: Sb3+ with widely tunable red/green/blue/white luminescence. Extrinsic Sb3+ dopants provide host another active sites to capture photo-generated excitons, thus triggering blue/red dual emission. Moreover, a reversible thermal-induced phase transition transforms blue/red emission into green/red dual emission. Both two phases exhibit intriguing excitation-wavelength dependent emission, affording a whole color gamut covering the red-green-blue (RGB) color triangle on the CIE 1931 diagram. Experimental and theoretical calculation studies reveal two emitters work independently, which paves the way for the multimode optical control and promotes the development of multifunctional luminescent materials.
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
Authors: Boninsegna Lorenzo , Yildirim Asli , Polles Guido , Zhan Yuxiang , Quinodoz Sofia A. , Finn Elizabeth H. , Guttman Mitchell , Zhou Xianghong Jasmine , Alber Frank 
Published: July 2022

AbstractA multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency (‘rare’) interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package.
Reference database of teeth images from the Family Bovidae
Authors: Brophy Juliet K. , Matthews Gregory J. 
Published: July 2022

AbstractResearchers typically rely on fossils from the Family Bovidae to generate African paleoenvironmental reconstructions due to their strict ecological tendencies. Bovids have dominated the southern African fauna for the past four million years and, therefore, dominate the fossil faunal assemblages, especially isolated teeth. Traditionally, researchers reference modern and fossil comparative collections to identify teeth. However, researchers are limited by the specific type and number of bovids at each institution. B.O.V.I.D. (Bovidae Occlusal Visual IDentification) is a repository of images of the occlusal surface of bovid teeth. The dataset currently includes extant bovids from 7 tribes and 20 species (~3900). B.O.V.I.D. contains two scaled images per specimen: a color and a black and white (binarized) image. The database is a useful reference for identifying bovid teeth. The large sample size also allows one to observe the natural variation that exists in each taxa. The binarized images can be used in statistical shape analyses, such as taxonomic classification. B.O.V.I.D. is a valuable supplement to other methods for taxonomically identifying bovid teeth.
Cell mediated remodeling of stiffness matched collagen and fibrin scaffolds
Authors: Jagiełło Alicja , Castillo Ulysses , Botvinick Elliot 
Published: July 2022

AbstractCells are known to continuously remodel their local extracellular matrix (ECM) and in a reciprocal way, they can also respond to mechanical and biochemical properties of their fibrous environment. In this study, we measured how stiffness around dermal fibroblasts (DFs) and human fibrosarcoma HT1080 cells differs with concentration of rat tail type 1 collagen (T1C) and type of ECM. Peri-cellular stiffness was probed in four directions using multi-axes optical tweezers active microrheology (AMR). First, we found that neither cell type significantly altered local stiffness landscape at different concentrations of T1C. Next, rat tail T1C, bovine skin T1C and fibrin cell-free hydrogels were polymerized at concentrations formulated to match median stiffness value. Each of these hydrogels exhibited distinct fiber architecture. Stiffness landscape and fibronectin secretion, but not nuclear/cytoplasmic YAP ratio differed with ECM type. Further, cell response to Y27632 or BB94 treatments, inhibiting cell contractility and activity of matrix metalloproteinases, respectively, was also dependent on ECM type. Given differential effect of tested ECMs on peri-cellular stiffness landscape, treatment effect and cell properties, this study underscores the need for peri-cellular and not bulk stiffness measurements in studies on cellular mechanotransduction.
Periodically taken photographs reveal the effect of pollinator insects on seed set in lotus flowers
Authors: Nagai Mihoko , Higuchi Yohei , Ishikawa Yusei , Guo Wei , Fukatsu Tokihiro , Baba Yuki G. , Takada Mayura B. 
Published: July 2022

AbstractUnderstanding of pollination systems is an important topic for evolutionary ecology, food production, and biodiversity conservation. However, it is difficult to grasp the whole picture of an individual system, because the activity of pollinators fluctuates depending on the flowering period and time of day. In order to reveal effective pollinator taxa and timing of visitation to the reproductive success of plants under the complex biological interactions and fluctuating abiotic factors, we developed an automatic system to take photographs at 5-s intervals to get near-complete flower visitation by pollinators during the entire flowering period of selected flowers ofNelumbo nuciferaand track the reproductive success of the same flowers until fruiting. Bee visits during the early morning hours of 05:00–07:59 on the second day of flowering under optimal temperatures with no rainfall or strong winds contributed strongly to seed set, with possible indirect negative effects by predators of the pollinators. Our results indicate the availability of periodic and consecutive photography system in clarifying the plant-pollinator interaction and its consequence to reproductive success of the plant. Further development is required to build a monitoring system to collect higher-resolution time-lapse images and automatically identify visiting insect species in the natural environment.
65,000-years of continuous grinding stone use at Madjedbebe, Northern Australia
Authors: Hayes Elspeth H. , Fullagar Richard , Field Judith H. , Coster Adelle C.F. , Matheson Carney , Nango May , Djandjomerr Djaykuk , Marwick Ben , Wallis Lynley A. , Smith Mike A. , Clarkson Chris 
Published: July 2022

AbstractGrinding stones and ground stone implements are important technological innovations in later human evolution, allowing the exploitation and use of new plant foods, novel tools (e.g., bone points and edge ground axes) and ground pigments. Excavations at the site of Madjedbebe recovered Australia’s (if not one of the world’s) largest and longest records of Pleistocene grinding stones, which span the past 65 thousand years (ka). Microscopic and chemical analyses show that the Madjedbebe grinding stone assemblage displays the earliest known evidence for seed grinding and intensive plant use, the earliest known production and use of edge-ground stone hatchets (aka axes), and the earliest intensive use of ground ochre pigments in Sahul (the Pleistocene landmass of Australia and New Guinea). The Madjedbebe grinding stone assemblage reveals economic, technological and symbolic innovations exemplary of the phenotypic plasticity of Homo sapiens dispersing out of Africa and into Sahul.
Retinal drusen counts are increased in inflammatory bowel disease, and with longer disease duration, more complications and associated IgA glomerulonephritis
Authors: Nicklason E. , Ham Y. , Ng D. , Glance S. , Abel K. , Harraka P. , Mack H. , Colville D. , Savige J. 
Published: July 2022

AbstractRetinal drusen are deposits of inflammatory proteins that are found in macular degeneration and glomerulonephritis and result, in part, from complement activation. This was a cross-sectional observational study of individuals with inflammatory bowel disease (IBD) recruited from a Gastroenterology clinic who underwent non-mydriatic retinal photography. Deidentified images were examined for drusen, and drusen counts and size were compared with matched controls, and examined for clinical associations. The cohort with IBD comprised 19 individuals with ulcerative colitis, 41 with Crohn’s disease and three with indeterminate colitis, including 34 males (54%) and an overall median age of 48 (IQR 23) years. Their median IBD duration was 7 (IQR 10) years, median CRP level was 7 (IQR 14) mg/L, and 28 (44%) had complications (fistula, stricture, bowel resection etc.), while 28 with Crohn’s disease (68%) had colonic involvement. Drusen counts were higher in IBD than controls (12 ± 34, 3 ± 8 respectively, p = 0.04). Counts ≥ 10 were also more common (14, 22%, and 4, 6%, p = 0.02, OR 4.21, 95%CI 1.30 to 13.63), and associated with longer disease duration (p = 0.01, OR 1.06, 95%CI 1.00 to 1.13), an increased likelihood of complications (p = 0.003, OR 6.90, 95%CI 1.69 to 28.15) and higher CRP levels at recruitment (p = 0.008, OR1.02, 95%CI 1.00 to 1.05). Increased retinal drusen were found in all four individuals with Crohn’s disease and IgA glomerulonephritis. IBD and drusen may share pathogenetic mechanisms and underlying risk factors such as complement activation.
Geriatric nutritional risk index is associated with retinopathy in patients with type 2 diabetes
Authors: Cho AJin , Hong Yun Soo , Park Hayne Cho , Kim Do Hyoung , Shin Young Joo , Lee Young-Ki 
Published: July 2022

AbstractThe geriatric nutritional risk index (GNRI) is a nutrition-related risk assessment tool and has been used in various clinical settings. The relationship between body mass index (BMI) and the associated risk of diabetic retinopathy (DR) remains inconclusive. We aimed to evaluate the association between GNRI and DR in patients with type 2 diabetes. We included a total of 1359 patients with type 2 diabetes who followed up in our diabetes clinic and underwent fundus photographic examinations from August 2006 to February 2014. DR was assessed by retinal ophthalmologists using comprehensive ophthalmologic examinations. Patients were divided into tertiles according to their GNRI category. Patients in a lower GNRI tertile tended to have a higher proportion of nonproliferative DR (NPDR) and proliferative DR (PDR) compared with those in the other tertiles. The risk of PDR was higher in patients included in GNRI tertile 1 (Odds ratio (OR) 2.252, 95% Confidence Interval (CI) 1.080–4.823, P = 0.033) and GNRI tertile 2 (OR 2.602, 95% CI 1.323–5.336, P = 0.007) compared with those in GNRI tertile 3. In patients with lower GNRIs, the prevalence of DR was higher than in those with higher GNRIs. When GNRI was compared with BMI using the area under the curve, overall accuracy was high in GNRI. The risk of PDR was high in patients with low GNRI and there is an inverse association between GNRI scores and prevalence of DR. GNRI might be a useful tool to predict DR in patients with type 2 diabetes.
Machine learning techniques for identification of carcinogenic mutations, which cause breast adenocarcinoma
Authors: Shah Asghar Ali , Malik Hafiz Abid Mahmood , Mohammad AbdulHafeez , Khan Yaser Daanial , Alourani Abdullah 
Published: July 2022

AbstractBreast adenocarcinoma is the most common of all cancers that occur in women. According to the United States of America survey, more than 282,000 breast cancer patients are registered each year; most of them are women. Detection of cancer at its early stage saves many lives. Each cell contains the genetic code in the form of gene sequences. Changes in the gene sequences may lead to cancer. Replication and/or recombination in the gene base sometimes lead to a permanent change in the nucleotide sequence of the genome, called a mutation. Cancer driver mutations can lead to cancer. The proposed study develops a framework for the early detection of breast adenocarcinoma using machine learning techniques. Every gene has a specific sequence of nucleotides. A total of 99 genes are identified in various studies whose mutations can lead to breast adenocarcinoma. This study uses the dataset taken from 4127 human samples, including men and women from more than 12 cohorts. A total of 6170 mutations in gene sequences are used in this study. Decision Tree, Random Forest, and Gaussian Naïve Bayes are applied to these gene sequences using three evaluation methods: independent set testing, self-consistency testing, and tenfold cross-validation testing. Evaluation metrics such as accuracy, specificity, sensitivity, and Mathew’s correlation coefficient are calculated. The decision tree algorithm obtains the best accuracy of 99% for each evaluation method.
Cationic protein 8 plays multiple roles in Galleria mellonella immunity
Authors: Kordaczuk Jakub , Sułek Michał , Mak Paweł , Zdybicka-Barabas Agnieszka , Śmiałek Justyna , Wojda Iwona 
Published: July 2022

AbstractGalleria mellonellacationic protein 8 (GmCP8) is a hemolymph protein previously identified as an opsonin and an inhibitor of fungal proteases. In this work, we showed its bactericidal activity towardPseudomonas entomophila,Pseudomonas aeruginosa,Bacillus thuringiensis,Staphylococcus aureus, andEscherichia coliand against yeast-like fungiCandida albicans. The activity againstE. coliwas correlated with bacterial membrane permeabilization. In turn, in the case ofP. entomophila,B. thuringiensis,andC. albicans, the atomic force microscopy analysis of the microbial surface showed changes in the topography of cells and changes in their nanomechanical properties. GmCP8 also showed the inhibitory activity toward the serine protease trypsin and the metalloproteinase thermolysin. The expression of the gene encoding the GmCP8 protein did not increase either in the gut or in the fat body ofG. mellonellaafter oral infection withP. entomophila. Similarly, the amount of GmCP8 in the hemolymph ofG. mellonelladid not change in immune-challenged insects. However, when GmCP8 was injected into theG. mellonellahemocel, a change in the survival curve was observed in the infected larvae. Our results shed new light on the function of GmCP8 protein in insect immunity, indicating its role in humoral defence mechanisms.
Missing eddy feedback may explain weak signal-to-noise ratios in climate predictions
Authors: Hardiman Steven C. , Dunstone Nick J. , Scaife Adam A. , Smith Doug M. , Comer Ruth , Nie Yu , Ren Hong-Li 
Published: July 2022

AbstractThe signal-to-noise paradox that climate models are better at predicting the real world than their own ensemble forecast members highlights a serious and currently unresolved model error, adversely affecting climate predictions and introducing uncertainty into climate projections. By computing the magnitude of feedback between transient eddies and large-scale flow anomalies in multiple seasonal forecast systems, this study shows that current systems underestimate this positive eddy feedback, and that this deficiency is strongly linked to weak signal-to-noise ratios in ensemble mean predictions. Improved eddy feedback is further shown to be linked to greater teleconnection strength between the El Niño Southern Oscillation and the Arctic Oscillation and to stronger predictable signals. We also present a technique to estimate the potential gain in skill that may come from eliminating eddy feedback deficiency, showing that skill could double in some extratropical regions, significantly improving predictions of the Arctic Oscillation.
Single image reflection removal through multi‐scale gradient refinement
Authors: Cheng Kuanhong , Du Juan , Li Jia , Li Yuxin , Li Yilan , Li Junhuai 
Published: July 2022

AbstractRemoving the undesired reflection layer from images taken through glass windows is an important yet challenging task. Many existing CNN‐based methods try to utilize the gradient as an important clue to guide the training and achieve better separation. But the scene depth of real‐world scenarios is usually uncontrollable, leading to the uncertainty of smooth level in the transmission and reflection layers, which makes it a great challenge to model the two layers in the gradient domain. This paper proposes a multi‐scale gradient refinement network to resolve this problem. First, it is suggested that even the two layers are usually partially smooth, their gradients can still be sharp in the down‐scaled samples. To this end, the separation is conducted at four different scales by minimizing the similarity of the two layers to boost the gradient sharpness prior. Second, it is considered that the separation performance of downscaled samples is usually superior to that of the high‐resolution images because of the sharper edges. For this reason, a cascade architecture is designed that takes the down‐scaled predictions to promote the high‐resolution decomposition stage‐by‐stage to recover the full‐resolution results. Besides, the scale‐wise memory mechanism is introduced into the prediction network to resolve the detail loss issue caused by the multi‐stage upscaling refinement process. The experimental results on benchmark datasets indicate that the new model surpasses several state‐of‐the‐art methods.
Career burnout and psychological consistency among radiation workers in China: a cross section study
Authors: Cui L. , Feng Z. , Xu H. 
Published: July 2022

We conducted a survey on the mental status, including burnout, sense of coherence (SOC) and anxiety about radiation exposure among medical radiation workers in China. SOC levels were evaluated through a validated scale, SOC-13. Burnout was measured using the 22-item version of Maslach Burnout Inventory Human Services Survey for Medical Personnel (MBI-HSS). A total of 277 medical radiation workers answered the questionnaire. The mean values of SOC-13 and burnout were 50 (SD 13.5) and 79.7 (SD 25.7), respectively. The sum scores of SOC-13 and MBI-HSS were significantly linear correlated (p < 0.01, F = 284.239, adjusted R2 = 0.506). Anxiety about radiation exposure was significantly associated with intention to leave employment (
χ

2 = 66.535, p < 0.001, Cramer’s v = 0.347, p < 0.001). The participants who have no anxiety about radiation exposure have significantly higher scores of sense of coherence than those who have mild and moderate anxiety (p < 0.01); they have lower scores of burnout (p < 0.01). The participants who have no intention to leave employment have significantly higher scores of sense of coherence and lower scores of burnout than those who have an intention or hesitate to leave (p < 0.01).
Most participants in this study showed considerable caution about whether to participate in radiation work during pregnancy. Anxiety about radiation exposure was considered a contributing factor for burnout and led to the intention to leave employment. Efforts to design targeted interventions, such as educational programs, to mitigate radiation anxiety in medical radiation workers are warranted.
Immature Platelet Fraction and Thrombin Generation: Preeclampsia Biomarkers
Authors: Moraes Daniela , Milioni Camila , Vieira Carolina Friske , Parera Eveline Avila , Silva Bárbara Dewes , Baron Miriam Viviane , Costa Bartira Ercília Pinheiro da , Poli-de-Figueiredo Carlos Eduardo 
Published: July 2022

AbstractPreeclampsia, a human pregnancy syndrome, is characterized by elevated blood pressure and proteinuria after the 20th week of gestation. Its etiology remains unknown, and its pathophysiological mechanisms are related to placental hypoperfusion, endothelial dysfunction, inflammation, and coagulation cascade activation. Recently, the role of the complement system has been considered. This syndrome is one of the main causes of maternal and fetal mortality and morbidity. This article discusses the hypothesis of preeclampsia being triggered by the occurrence of inadequate implantation of the syncytiotrophoblast, associated with bleeding during the first stage of pregnancy and with augmented thrombin generation. Thrombin activates platelets, increasing the release of antiangiogenic factors and activating the complement system, inducing the membrane attack complex (C5b9). Immature platelet fraction and thrombin generation may be possible blood biomarkers to help the early diagnosis of preeclampsia.