bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pro-inflammatory microenvironment and systemic accumulation of CXCR3+ cell exacerbate lung pathology of old rhesus macaques infected with SARS-CoV-2
Authors: Zheng Hong-Yi , He Xiao-Yan , Li Wei , Song Tian-Zhang , Han Jian-Bao , Yang Xiang , Liu Feng-Liang , Luo Rong-Hua , Tian Ren-Rong , Feng Xiao-Li , Ma Yu-Hua , Liu Chao , Li Ming-Hua , Zheng Yong-Tang 
Published: September 2021

AbstractUnderstanding the pathological features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in an animal model is crucial for the treatment of coronavirus disease 2019 (COVID-19). Here, we compared immunopathological changes in young and old rhesus macaques (RMs) before and after SARS-CoV-2 infection at the tissue level. Quantitative analysis of multiplex immunofluorescence staining images of formalin-fixed paraffin-embedded (FFPE) sections showed that SARS-CoV-2 infection specifically induced elevated levels of apoptosis, autophagy, and nuclear factor kappa-B (NF-κB) activation of angiotensin-converting enzyme 2 (ACE2)+ cells, and increased interferon α (IFN-α)- and interleukin 6 (IL-6)-secreting cells and C-X-C motif chemokine receptor 3 (CXCR3)+ cells in lung tissue of old RMs. This pathological pattern, which may be related to the age-related pro-inflammatory microenvironment in both lungs and spleens, was significantly correlated with the systemic accumulation of CXCR3+ cells in lungs, spleens, and peripheral blood. Furthermore, the ratio of CXCR3+ to T-box protein expression in T cell (T-bet)+ (CXCR3+/T-bet+ ratio) in CD8+ cells may be used as a predictor of severe COVID-19. These findings uncovered the impact of aging on the immunopathology of early SARS-CoV-2 infection and demonstrated the potential application of CXCR3+ cells in predicting severe COVID-19.
Safety and tolerability of lenalidomide maintenance in post-transplant acute myeloid leukemia and high-risk myelodysplastic syndrome
Authors: Pham Brian , Hoeg Rasmus , Krishnan Rajeev , Richman Carol , Tuscano Joseph , Abedi Mehrdad 
Published: September 2021

AbstractRelapse after allogeneic stem cell transplant in unfavorable-risk acute myeloid leukemia (AML) and high-risk myelodysplastic syndrome (MDS) portends a poor prognosis. We conducted a single-center phase I dose-escalation study with lenalidomide maintenance in high-risk MDS and AML patients after allogeneic transplantation. Sixteen patients enrolled in a “3 + 3” study design starting at lenalidomide 5 mg daily, increasing in increments of 5 mg up to 15 mg. Lenalidomide was given for 21 days of a 28-day cycle for a total of six cycles. Most common dose-limiting toxicities were lymphopenia, diarrhea, nausea, and neutropenia. Two patients had acute graft-versus-host disease (GVHD), and five patients developed chronic GVHD. The maximum tolerated dose was 10 mg, after dose-limiting toxicities were seen in the 15 mg group. Two dose-limiting toxicities were seen from development of acute GVHD and grade III diarrhea. Limitations of the study include time to initiation at 6 months post transplant, as many high-risk patients will have relapsed within this time frame before starting maintenance lenalidomide. Overall, lenalidomide was well tolerated with minimal GVHD and low rates of relapse rates, warranting further study.
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution
Authors: Zhang Yongxia , Zhang Guo-Qiang , Zhang Diyang , Liu Xue-Die , Xu Xin-Yu , Sun Wei-Hong , Yu Xia , Zhu Xiaoen , Wang Zhi-Wen , Zhao Xiang , Zhong Wen-Ying , Chen Hongfeng , Yin Wei-Lun , Huang Tengbo , Niu Shan-Ce , Liu Zhong-Jian 
Published: September 2021

AbstractAs one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.
High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy
Authors: Gao Yuhao , Yang Qinsong , Yan Xinhui , Wu Xinyue , Yang Feng , Li Jianzhao , Wei Jia , Ni Junbei , Ahmad Mudassar , Bai Songling , Teng Yuanwen 
Published: September 2021

AbstractDormancy-associated MADS-box(DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pearDAMgenes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pearDAMgenes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects ofDAMgenes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.
Rational design of hyperstable antibacterial peptides for food preservation
Authors: Vishweshwaraiah Yashavantha L. , Acharya Abhishek , Hegde Vinayak , Prakash Balaji 
Published: September 2021

AbstractWe describe the design of peptides with properties like thermostability, pH stability, and antibacterial activity against a few bacterial food pathogens. Insights obtained from classical structure-function analysis of natural peptides and their mutants through antimicrobial and enzymatic assays are used to rationally develop a set of peptides. pH and thermostability assays were performed to demonstrate robust antimicrobial activity post-treatment with high temperatures and at wide pH ranges. We have also investigated the mode of action of these hyperstable peptides using membrane permeability assays, electron microscopy, and molecular dynamics simulations. Notably, through mutational studies, we show that these peptides elicit their antibacterial action via both membrane destabilization and inhibition of intracellular trypsin—the two functions attributable to separate peptide segments. Finally, toxicity studies and food preservation assays demonstrate the safety and efficacy of the designed peptides for food preservation. Overall, the study provides a general ‘blueprint’ for the development of stable antimicrobial peptides (AMPs). Insights obtained from this work may also be combined with combinatorial methods in high-throughput studies for future development of antimicrobials for various applications.
Measuring the density structure of an accretion hot spot
Authors: Espaillat C. C. , Robinson C. E. , Romanova M. M. , Thanathibodee T. , Wendeborn J. , Calvet N. , Reynolds M. , Muzerolle J. 
Published: September 2021

AbstractMagnetospheric accretion models predict that matter from protoplanetary disks accretes onto stars via funnel flows, which follow stellar magnetic field lines and shock on the stellar surfaces1–3, leaving hot spots with density gradients4–6. Previous work has provided observational evidence of varying density in hot spots7, but these observations were not sensitive to the radial density distribution. Attempts have been made to measure this distribution using X-ray observations8–10; however, X-ray emission traces only a fraction of the hot spot11,12 and also coronal emission13,14. Here we report periodic ultraviolet and optical light curves of the accreting star GM Aurigae, which have a time lag of about one day between their peaks. The periodicity arises because the source of the ultraviolet and optical emission moves into and out of view as it rotates along with the star. The time lag indicates a difference in the spatial distribution of ultraviolet and optical brightness over the stellar surface. Within the framework of a magnetospheric accretion model, this finding indicates the presence of a radial density gradient in a hot spot on the stellar surface, because regions of the hot spot with different densities have different temperatures and therefore emit radiation at different wavelengths.
A high-spatial-resolution dataset of human thermal stress indices over South and East Asia
Authors: Yan Yechao , Xu Yangyang , Yue Shuping 
Published: September 2021

AbstractThermal stress poses a major public health threat in a warming world, especially to disadvantaged communities. At the population group level, human thermal stress is heavily affected by landscape heterogeneities such as terrain, surface water, and vegetation. High-spatial-resolution thermal-stress indices, containing more detailed spatial information, are greatly needed to characterize the spatial pattern of thermal stress to enable a better understanding of its impacts on public health, tourism, and study and work performance. Here, we present a 0.1° × 0.1° gridded dataset of multiple thermal stress indices derived from the newly available ECMWF ERA5-Land and ERA5 reanalysis products over South and East Asia from 1981 to 2019. This high-spatial-resolution database of human thermal stress indices over South and East Asia (HiTiSEA), which contains the daily mean, maximum, and minimum values of UTCI, MRT, and eight other widely adopted indices, is suitable for both indoor and outdoor applications and allows researchers and practitioners to investigate the spatial and temporal evolution of human thermal stress and its impacts on densely populated regions over South and East Asia at a finer scale.
Marangoni effect inspired robotic self-propulsion over a water surface using a flow-imbibition-powered microfluidic pump
Authors: Kwak Bokeon , Choi Soyoung , Maeng Jiyeon , Bae Joonbum 
Published: September 2021

AbstractCertain aquatic insects rapidly traverse water by secreting surfactants that exploit the Marangoni effect, inspiring the development of many self-propulsion systems. In this research, to demonstrate a new way of delivering liquid fuel to a water surface for Marangoni propulsion, a microfluidic pump driven by the flow-imbibition by a porous medium was integrated to create a novel self-propelling robot. After triggered by a small magnet, the liquid fuel stored in a microchannel is autonomously transported to an outlet in a mechanically tunable manner. We also comprehensively analyzed the effects of various design parameters on the robot’s locomotory behavior. It was shown that the traveled distance, energy density of fuel, operation time, and motion directionality were tunable by adjusting porous media, nozzle diameter, keel-extrusion, and the distance between the nozzle and water surface. The utilization of a microfluidic device in bioinspired robot is expected to bring out new possibilities in future development of self-propulsion system.
Neural activity in the human anterior thalamus during natural vision
Authors: Leszczynski Marcin , Chaieb Leila , Staudigl Tobias , Enkirch Simon Jonas , Fell Juergen , Schroeder Charles E. 
Published: September 2021

AbstractIn natural vision humans and other primates explore environment by active sensing, using saccadic eye movements to relocate the fovea and sample different bits of information multiple times per second. Saccades induce a phase reset of ongoing neuronal oscillations in primary and higher-order visual cortices and in the medial temporal lobe. As a result, neuron ensembles are shifted to a common state at the time visual input propagates through the system (i.e., just after fixation). The extent of the brain’s circuitry that is modulated by saccades is not yet known. Here, we evaluate the possibility that saccadic phase reset impacts the anterior nuclei of the thalamus (ANT). Using recordings in the human thalamus of three surgical patients during natural vision, we found that saccades and visual stimulus onset both modulate neural activity, but with distinct field potential morphologies. Specifically, we found that fixation-locked field potentials had a component that preceded saccade onset. It was followed by an early negativity around 50 ms after fixation onset which is significantly faster than any response to visual stimulus presentation. The timing of these events suggests that the ANT is predictively modulated before the saccadic eye movement. We also found oscillatory phase concentration, peaking at 3–4 Hz, coincident with suppression of Broadband High-frequency Activity (BHA; 80–180 Hz), both locked to fixation onset supporting the idea that neural oscillations in these nuclei are reorganized to a low excitability state right after fixation onset. These findings show that during real-world natural visual exploration neural dynamics in the human ANT is influenced by visual and oculomotor events, which supports the idea that ANT, apart from their contribution to episodic memory, also play a role in natural vision.
Reallocation of water resources according to social, economic, and environmental parameters
Authors: Rezaee Alireza , Bozorg-Haddad Omid , Chu Xuefeng 
Published: September 2021

AbstractPopulation growth, urbanization, and industrial development have significantly increased water demands in many countries, raising the concerns about water resources sustainability to meet the needs of humans and the environment. Furthermore, the economy-oriented allocation of water resources has caused many socio-environmental problems. The main goal of this study is to develop a system dynamics modeling framework that integrates economic, social, and environmental dimensions for the decision of water resources allocation. The Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) is used to rank modeling scenarios and identify the best strategy for water allocation. In the application to East Azerbaijan province of Iran, six industry groups (including chemical, food and beverage, non-metal, machinery and equipment, metal, and textile), thirteen water allocation scenarios, and five criteria (including profit index, employment index, return of surface water, groundwater sustainability index, and total allocated water) were considered. The TOPSIS results showed that in the best scenario most water was allocated to the non-metal industry with a relative distance of 0.63 to the ideal solution. On the other hand, the current water allocation scenario ranked seventh, indicating that significant improvements are required to take into account the social, economic, and environmental factors for optimal reallocation of water resources among different industry users.
Efficacy of a comprehensive binary classification model using a deep convolutional neural network for wireless capsule endoscopy
Authors: Kim Sang Hoon , Hwang Youngbae , Oh Dong Jun , Nam Ji Hyung , Kim Ki Bae , Park Junseok , Song Hyun Joo , Lim Yun Jeong 
Published: September 2021

AbstractThe manual reading of capsule endoscopy (CE) videos in small bowel disease diagnosis is time-intensive. Algorithms introduced to automate this process are premature for real clinical applications, and multi-diagnosis using these methods has not been sufficiently validated. Therefore, we developed a practical binary classification model, which selectively identifies clinically meaningful images including inflamed mucosa, atypical vascularity or bleeding, and tested it with unseen cases. Four hundred thousand CE images were randomly selected from 84 cases in which 240,000 images were used to train the algorithm to categorize images binarily. The remaining images were utilized for validation and internal testing. The algorithm was externally tested with 256,591 unseen images. The diagnostic accuracy of the trained model applied to the validation set was 98.067%. In contrast, the accuracy of the model when applied to a dataset provided by an independent hospital that did not participate during training was 85.470%. The area under the curve (AUC) was 0.922. Our model showed excellent internal test results, and the misreadings were slightly increased when the model was tested in unseen external cases while the classified ‘insignificant’ images contain ambiguous substances. Once this limitation is solved, the proposed CNN-based binary classification will be a promising candidate for developing clinically-ready computer-aided reading methods.
Creation, evolution, and dissolution of social groups
Authors: Flamino James , Szymanski Boleslaw K. , Bahulkar Ashwin , Chan Kevin , Lizardo Omar 
Published: September 2021

AbstractUnderstanding why people join, stay, or leave social groups is a central question in the social sciences, including computational social systems, while modeling these processes is a challenge in complex networks. Yet, the current empirical studies rarely focus on group dynamics for lack of data relating opinions to group membership. In the NetSense data, we find hundreds of face-to-face groups whose members make thousands of changes of memberships and opinions. We also observe two trends: opinion homogeneity grows over time, and individuals holding unpopular opinions frequently change groups. These observations and data provide us with the basis on which we model the underlying dynamics of human behavior. We formally define the utility that members gain from ingroup interactions as a function of the levels of homophily of opinions of group members with opinions of a given individual in this group. We demonstrate that so-defined utility applied to our empirical data increases after each observed change. We then introduce an analytical model and show that it accurately recreates the trends observed in the NetSense data.
Arsenic leads to autophagy of keratinocytes by increasing aquaporin 3 expression
Authors: Yu Sebastian , Li Ling-Hau , Lee Chih-Hung , Jeyakannu Palaniraja , Wang Jeh-Jeng , Hong Chien-Hui 
Published: September 2021

AbstractExposure to arsenic, a ubiquitous metalloid on Earth, results in human cancers. Skin cancer is the most common arsenical cancers. Both autophagy and aquaporin pathway are known to promote carcinogenesis. However, the mechanisms by which arsenic regulates aquaporin and autophagy in arsenical skin cancers remain elusive. This study aims to address how arsenic regulates aquaporin-3, the predominant aquaporin in epidermal keratinocytes, and how this process would induce autophagy. Quantitative real-time PCR and immunofluorescence were used to measure the expression of aquaporin 3 in arsenical skin cancers and arsenic-treated keratinocytes. Beclin-1 expression and autophagy were measured. We examined if blocking aquaporin 3 could interfere arsenic-induced autophagy in keratinocytes. Expression of aquaporin 3 is increased in arsenical cancers and in arsenic-treated keratinocytes. Arsenic induced autophagy in primary human keratinocytes. Notably, the arsenic-induced autophagy was inhibited by pretreatment of keratinocytes with aquaporin inhibitors Auphen or AgNO3, or RNA interference against aquaporin 3. The data indicates that the aquaporin 3 is an important cell membrane channel to mediate arsenic uptake and contributes to the arsenic-induced autophagy.
Automated processing of thermal imaging to detect COVID-19
Authors: Brzezinski Rafael Y. , Rabin Neta , Lewis Nir , Peled Racheli , Kerpel Ariel , Tsur Avishai M. , Gendelman Omer , Naftali-Shani Nili , Gringauz Irina , Amital Howard , Leibowitz Avshalom , Mayan Haim , Ben-Zvi Ilan , Heller Eyal , Shechtman Liran , Rogowski Ori , Shenhar-Tsarfaty Shani , Konen Eli , Marom Edith M. , Ironi Avinoah , Rahav Galia , Zimmer Yair , Grossman Ehud , Ovadia-Blechman Zehava , Leor Jonathan , Hoffer Oshrit 
Published: September 2021

AbstractRapid and sensitive screening tools for SARS-CoV-2 infection are essential to limit the spread of COVID-19 and to properly allocate national resources. Here, we developed a new point-of-care, non-contact thermal imaging tool to detect COVID-19, based on advanced image processing algorithms. We captured thermal images of the backs of individuals with and without COVID-19 using a portable thermal camera that connects directly to smartphones. Our novel image processing algorithms automatically extracted multiple texture and shape features of the thermal images and achieved an area under the curve (AUC) of 0.85 in COVID-19 detection with up to 92% sensitivity. Thermal imaging scores were inversely correlated with clinical variables associated with COVID-19 disease progression. In summary, we show, for the first time, that a hand-held thermal imaging device can be used to detect COVID-19. Non-invasive thermal imaging could be used to screen for COVID-19 in out-of-hospital settings, especially in low-income regions with limited imaging resources.