bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of high-quality nuclei isolation to study plant root-microbe interaction for microfluidic single nuclei-transcriptomic sequencing
Authors: D’Agostino Leonidas W. , Yong-Villalobos Lenin , Herrera-Estrella Luis , Patil Gunvant B. 
Published: March 2023

Abstract
Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or developmental signals. In plants, this technology is being utilized to identify cell-type-specific trajectories for the study of several tissue types and important traits, including the single-cell dissection of the genetic determinants regulating plant-microbe interactions. The isolation of high-quality nuclei is one of the prerequisite steps to obtain high quality sNucRNA data and study gene expression at the single-cell level. Although nuclei isolation from several plant tissues is well established, this process is highly troublesome when plant tissues are associated with microorganism (bacterial or fungal). Therefore, isolation of microbe-free, high-quality nuclei from plant tissues is necessary to avoid clogging the microfluidic channel of droplet-based sNucRNA-seq platforms (e.g., 10X Genomics) and ensure accurate nuclei staining and counting. Here, we developed a simple, effective, and efficient method to isolate high-quality nuclei from soybean roots and root nodules. This protocol has been designed to be easily implemented into any lab environment, and it can also be scaled up for use with multiple samples and applicable to a variety of samples with the presence of microbes. We validated this protocol by successfully generating a barcoded library using the 10x genomics microfluidic platform from tissue subjected to this procedure. This workflow was developed to provide an accessible alternative without use of instrument-based approaches (e.g., fluorescent cell sorting) and will expand the ability of researchers to perform experiments such as sNucRNA-seq and sNucATAC-seq on inherently heterogeneous plant tissue samples.
Impact of THIONIL ® on reducing water and soil micropollutant and enhancement of growth, survival, antivibrio, immunity and health indices of Litopenaeus vannamei in pond trial
Authors: Thamarai Rajkumar , Sivaprakasam Thiyagarajan , Harikrishnan Dhatchayani , Prak Jawahar sri , Swaminathan Jeyashree , Subramanium Kalidass , Mani Koteeswaran , Prabhakaran Rajkumar , Sukumar Vimal 
Published: March 2023

Abstract
There is an urgent requisite for an improvement of the white leg shrimp Litopenaeus vannamei health related indices and immunity due to the emerging diseases. Recently, probiotics have been playing an important role in L. vannamei health management. Therefore, the current pond trail was to evaluate the probiotic proficiency of commercial probiotic product of THIONIL (THIO) on enhancement of the water, soil, growth, digestibility, survival, immune related indices and susceptibility of L. vannamei pond level trials. The study was carried out in the major shrimp culturing regions of Kavali, Nellore and Ponneri, Tamil Nadu, India. The experimental L. vannamei was divided into seven groups (1Lacks/ha), such as, negative control (THIO 0% - untreated), positive control (challenge with vibriosis) 2%, 4%, 6%, 8%, and 10% of THIO was encapsulated with commercial feed (CP Aqua). Bioassays were carried out in different day intervals includes, 0, 5, 25, 50, 100 and 123 for evaluating the productivity, anti-vibrio activity, digestive enzyme for digestibility, histological, immunological indices, and cytotoxicity in Artemia nauplii. The significant differences were observed in the increased growth (35.71 g/ shrimp) and digestive parameters in 10% THIO-fed shrimp, however, the other THIO-fed shrimp groups were also showed notable growth compared with control group. The results revealed that, the gill, hepatopancreas and gastro intestine have ha lesser tissue damage in 10% THIO when compared with control. The 10% THIO fed exhibited resistant potential against Vibrio parahaemolyticus (0.008 × 104 cfu/g) (AHPND-Acute Hepatopancreatic Necrosis Disease) and Vibrio harveyi (0.051×105 cfu/g) (Vibriosis). Additionally, 10% THIO fed shrimp revealed significant enhancement of immune related parameters when compared with control. In conclusion the results documented the THIO treatment shrimp had significant enhancement in the water and soil quality growth, strengthens the innate immunity and showed protection against Vibrio infections.
Mortality and Prognostic Factors for Spontaneous Pneumothorax in Older Adults: A Retrospective Study
Authors: Nishizawa Saori , Tobino Kazunori , Murakami Yousuke , Uchida Kazuki , Kawabata Takafumi , Ota Hiroyuki , Hiramatsu Yuri , Sueyasu Takuto , Tsuruno Kosuke 
Published: March 2023

Abstract
Background
Spontaneous pneumothorax occurs predominantly in young males and older adults, in whom it is often secondary to chronic obstructive pulmonary disease (COPD) or interstitial lung disease (ILDs) and can be refractory and fatal. We aimed to investigate the mortality and prognostic factors for pneumothorax in older patients.
Methods
We retrospectively studied patients with pneumothorax aged ≥ 65 years who visited our department from October 2012 to January 2019. Data on sex, age, medical history, smoking history, underlying lung disease, treatment, and prognosis were extracted from the medical records. Cox proportional hazards regression analysis was used to investigate pneumothorax mortality and prognostic factors.
Results
A total of 239 patients were included (median age, 78 years; 203 males and 36 females). Thirty-six patients (15%) died during hospitalisation, respiratory disease was the direct cause of death in 30 patients (83.3%), and 211 (88.3%) patients had underlying lung disease. The incidence of pneumonia in our hospital was 22.6% (54 cases), higher than previous reports (11%). On admission, the mortality rate was 33% (18/54) in patients with concomitant pneumonia; univariate analysis showed significant differences in the Charlson Comorbidity Index (CCI), activities of daily living (ADL), and concomitant pneumonia. Cox proportional hazard regression analyses for ADL, CCI, and concomitant pneumonia showed that concomitant pneumonia was the only independent predictor of death during hospitalisation (log-rank, p = 0.005).
Conclusion
Although COPD and ILDs are generally considered as mortality risks for pneumothorax, this study suggests that concomitant pneumonia at admission may be a mortality risk factor for pneumothorax.
DeTformer: A Novel Efficient Transformer Framework for Image Deraining
Authors: Ragini Thatikonda , Cheruku Ramalingaswamy , Prakash Kodali 
Published: March 2023

Abstract
Captured rainy images severely degrade outdoor vision systems performance, such as semi-autonomous or autonomous driving systems and video surveillance systems. Consequently, removing heavy and complex rain streaks i.e., undesirable rainy artifacts from a rainy image plays a crucial role for many high-level computer vision tasks and has drawn researchers’ attention from the past few years. The main drawbacks of Convolutional neural networks: have smaller receptive field, lack the model’s ability to capture long-range dependencies and complicated rainy artifacts, non-adaptive to input content and also computational complexity grows quadratically with input image size. These factors limit the deraining model performance improvement further. Recently, transformer has achieved better performance in both Natural language processing (NLP) and high-level computer vision (CV). We cannot adopt transformer directly to image deraining task as it has following limitations: a) although the transformer possesses powerful long-range computational capability, it lacks the ability to model local features b) to process input image, transformer uses fixed patch size, therefore pixels at the patch edges cannot use local features of surrounding pixels while removing heavy rain streaks. To address these issues, in single image deraining, we proposed a novel and efficient De-raining Transformer (DeTformer). In DeTformer, we designed a “Gated-Depth-wise Convolution Feed-forward Network” (GDWCFN) to address the first issue and applied depthwise convolution to improve the modelling capability of local features and suppress unnecessary features and allow only useful information further. Also, the second issue was addressed, by introducing multi-resolution features in our network, and we applied progressive learning in the transformer and thus it allows the edge pixels to utilize local features effectively. Furthermore, to integrate the extracted multi-scale features and provide feature interaction across channel dimensions, we introduced a “Multi-head Depth-wise Convolution Transposed Attention” (MDWCTA) module. The proposed model experimented with various de-rained datasets and compared with various state-of-the-art models. The experimental results show that DeTformer network achieves superior performance compared to state-of-the-art networks on synthetic and real-world rain datasets.
Isolation, characterization and anti-oxidant potential of melanin pigment from Trichomerium bhatii NFCCI 4305
Authors: Suthar Malika , Singh Sanjay K. 
Published: March 2023

Abstract
Melanin is usually formed by oxidative polymerization of phenolic compounds produced by bacteria, fungi, plants as well as animals. They have gained popularity for its multifarous properties and applications in various industries, especially the derma-cosmetic industries where fungal melanin has recently been highlighted as a potential source of natural bioactive compounds beneficial to skin and hair. The anti-oxidant potential and free radical scavenging activities of natural melanin makes them suitable for application in cosmetic products. In the present we have isolated and characterized a melanin pigment from Trichomerium bhatii NFCCI 4305, an unconventional fungus of Indian origin. The biological properties of purified melanin from the fungus were evaluated for its antioxidant activity. Following alkali acid treatment of the fermented broth, the pigment was extracted and further, its nature was confirmed as melanin through physico-chemical tests and spectral (UV and FTIR) analysis. The analysis of the elemental composition indicated that the pigment fall into DOPA category of melanin. The purified melanin showed a good DPPH (1, 1-Diphenyl-2-picrylhydrazyl) free radical-scavenging activity. To our understanding this is the first report on melanin characterization from the fungal genus Trichomerium.
Medical Communication Training: The Effect of Gender and Experience with Goals of Care Discussions
Authors: Dorough Ramona , Adamuti-Trache Maria , Sekar Dheepa , Siropaides Caitlin 
Published: March 2023

Abstract
Background. Communication skills are increasingly recognized as a crucial component of medical training. However, little is known about the efficacy of various training methods when considering diverse student backgrounds, such as gender and prior training experience (i.e., year of residency).
Objective. This study explores medical learners’ perception of effective communication in conducting goals of care (GOC) discussions with patients after receiving communication training as well as assessing for differences in preparedness for GOC discussions by gender and prior training experience.
Participants. A sample of 114 residents in either their first, second, or third year of internal medicine residency.
Main Measure. Participants participated in the communication training and completed pre- and –post- surveys on perceived effectiveness in GOC discussions.
Design. We employed multivariate analyses of the surveys.
Main Measures. The main measure was to examine residents’ perception of preparedness as defined by residents perceived effectiveness of care, confidence in having GOC discussions with patients, confidence in making recommendations that align with patient values, and the perceived value of GOC training.
Key Results. We found that after communication training most residents, regardless of gender or year of residency, felt more effective in having healthcare conversations with patients and making GOC healthcare recommendations. We also found that males and females reported differences in experiences in practicing GOC discussions depending on prior training in medical school.
Conclusion. The study also shows that the same curriculum is effective for residents at each level of training, but more research on the interaction effect between prior training and gender is needed.
Anomaly-Based Detection of Microarchitectural Attacks for IoT Devices
Authors: Li Congmiao , Gaudiot Jean-Luc 
Published: March 2023

Abstract
With the rapid growth of Internet of Things (IoT) technology, the number of connected devices and information processed through the Internet has significantly risen. As a result, cyber-attacks targeting vulnerable IoT devices have also dramatically increased. Microarchitectural attacks pose a serious threat to IoT security because they can not only leak confidential information to adversaries through shared processor resources such as caches, branch predictors and various functional units but also fully compromise the embedded system devices themselves. Traditional signature-based antivirus software cannot effectively detect microarchitectural attacks, particularly zero-day attacks. In this paper, an anomaly-based detector for IoT devices is developed to demonstrate the feasibility of detecting unknown microarchitectural attacks for resource-constrained devices using features collected from hardware performance counters with unsupervised machine learning and feature selection methods. Our experiments show promising detection results for the tested devices. The methodology will be used to guide the development of such detectors for similar IoT devices.
Monocytes Subsets Altered Distribution and Dysregulated Plasma hsa-miR-21-5p and hsa- miR-155-5p in HCV-Linked Liver Cirrhosis Progression to Hepatocellular Carcinoma
Authors: Hammad Reham , Dosoky Mona A El , Madbouly Asmaa A El , Aglan Reda Badr , Hamid Sherihan G Abdel , Zaki Samy , Ali Elham , Hakem Fatma Al Zahraa Abdel , Mosaad Alshimaa M , Mageed Neamat A Abdel , Kotb Fatma M , Kotb Hend G , Aboul-Kheir Omaima I , Kujumdshiev Sandy , Sack Ulrich , Lambert Claude , Hamdy Nadia M. 
Published: March 2023

Abstract
Cirrhosis-associated immune dysfunction (CAID) is an
immunological perturbation that develops on top of liver cirrhosis
(LC). Immune perturbation directs LC progression to hepatocellular
carcinoma (HCC). Innate immune cells, in particular, monocytes,
play key roles in inflammation and tumorigenesis. MicroRNAs (miRs)
have been regarded as master regulators of the immune networks. We
aim to investigate the altered monocytes subsets distribution in LC
and subsequent HCC in association with the expression level of
plasma homo sapiens (hsa)-miR-21-5p and hsa-miR-155-5p. A step
toward non-protein coding (nc) RNA precision medicine based on the
immune perturbation, manifested as altered monocytes distribution,
on top of LC and HCC. Subjects and Methods: Seventy-nine patients
diagnosed with chronic hepatitis C virus (CHCV) infection with LC
were enrolled in the current study. Patients were sub-classified
into LC group without HCC (n=40), LC with HCC (n=39), and 15
apparently healthy controls. Monocyte subsets frequencies were
assessed by flow-cytometry. Real-time quantitative PCR was used to
measure plasma hsa-miR-21-5p and hsa-miR-155-5p expression.
Results: hsa-miR-21-5p correlated with intermediate monocytes
(r=0.30, p=0.007), while hsa-miR-155-5p negatively
correlated with nonclassical monocytes (r= -0.316,
p=0.005). ROC curve analysis revealed that combining
intermediate monocytes frequency and hsa-miR-21 yielded
sensitivity= 79.5%, specificity= 75%, and AUC= 0.84. In comparison,
AFP yielded a lower sensitivity = 69% and 100% specificity with
AUC= 0.85. Logistic regression analysis proved that up-regulation
of intermediate monocytes frequency and hsa-miR-21-5p were
independent risk factors for LC progression to HCC, after
adjustment for co-founders. Conclusion: Monocyte subsets
differentiation in HCC was linked to hsa-miR-21-5p and
hsa-miR-155-5p. Combined up-regulation of intermediate monocytes
frequency and hsa-miR-21-5p expression could be considered a
sensitive indicator of LC development to HCC. Circulating
intermediate monocytes and hsa-miR-21-5p were independent risk
factors for HCC evolution, clinically and in
silicoproofed.
Integration of skin phenome and microbiome reveals the ­key role of bacteria in human skin aging
Authors: Xia Jingjing , Li Zhiming , Zhong Qian , Wei Qingzhen , Jiang Liuyiqi , Duan Cheng , Jia Huijue , Tan Yimei , Han Lianyi , Wang Jiucun , Liu Xiao 
Published: March 2023

Abstract
Background: Despite the complexity, distinct ecological niches are believed to primarily drive the skin microbiome composition. Meanwhile, skin aging is a dynamic process with a spectrum of phenotypical changes, making it an attractive model for studying microbiome-phenotype interactions. Although a large number of studies confirmed the impact of chronological age in skin bacterial communities, the understanding of cross-kingdom microbiome variation with skin aging remains minimal. And this is not trivial because one’s skin condition or perceived age may deviate largely from their actual age as skin aging is a complex process combining chronological and extrinsic aging.
Results: To this end, 822 facial microbial samples and skin phenotypes from the corresponding area were assessed in a Chinese cohort, the largest population size to date for skin shotgun metagenomic profiling. Our data revealed that among 14 measured variables, porphyrin and chronological age explained the most significant microbial variability. Consistent with previous studies based on 16S rRNA gene sequencing, we revealed increased biodiversity with aging and further specified age-associated species across kingdoms. While the abundance of most bacteria increased with age, two species, Cutibacterium acnes and Aeromicrobium choanae, declined. Microbiome undergoes active function selection from energy demands/growth to stress adaptation along aging. In addition, we characterized microbial changes in skin aging, asa combined consequence of both intrinsic and extrinsic reasons and reflecting the actual dynamic of niche conditions rather than chronological age. Using the multiple linear regression model, we predicted premature-aging/delayed-aging-related microbial species, mainly localizing to Moraxella osloensis and C. acnes. Furthermore, we validated the biological functions in vitro of some host-microbe interactions predicted by the microbiome-skin phenome association network. M. osloensis regulated collagen metabolism, extracellular matrix assembly and promoted cell senescence in human keratinocyte and fibroblast cells.
Conclusions: We presume that application of both culture-independent and culture-dependent approaches can advance a good understanding of microbiome-phenotype interactions. Our study is of significance for designing interventions against aging-related skin conditions.
Efficacy analysis of axillary approach in the treatment of Ideberg type I and II scapular glenoid fractures
Authors: Ding Hao , Bao YonGang , Yin Bo , Chang Qing Hua , Zai Qing Shu , Shi Qiang , Hu Hua Jian , Wang Hai Bin , Zhao Yi Feng , Song Fu Qiang , Wu Bin 
Published: March 2023

AbstractBackground:To investigate the clinical efficacy of the axillary approach in the surgical treatment of Ideberg type I and II scapular glenoid fractures.Methods:Retrospective analysis of 13 cases of scapular glenoid fracture treated in the affiliated Hospital of Jining Medical College, Jiaxiang County People hospital, Zoucheng City people Hospital, Yanzhou District People Hospital, and Juancheng County people Hospital from December 2020 to January 2022. Eight males (including one bilateral) and five females, with an average age of 57.5 years (range from 33 to 75 years). According to Ideberg classification, there were 10 cases of type Ⅰ a, 1 case of type Ⅰ a combined with type Ⅰ b, and 2 cases of type Ⅱ. All patients were treated with axillary approach surgery and seven patients with combined anterior shoulder dislocation were treated by first-stage manipulation and second-stage reoperation. Seven patients were fixed with a wire anchor, three patients with type Ⅰ a were fixed with a "T" plate, and five patients were complicated with rotator cuff tear and were repaired with a wire anchor. At the last follow-up, the Constant-Murley shoulder function score, visual analog score (VAS), DASH score, and Hawkins grade were used to evaluate shoulder function, pain, and stability after treatment.Results:All 13 patients in this group were followed up thoroughly, and the follow-up time was 12-25 months, with an average of 18.6 months. The operation time was 65-135min, with an average of 85.6 min. Intraoperative blood loss ranged from 20 to 120mL, averaging 55.6ml. The duration of hospitalization ranged from 7 to 22 days, with an average of 9.6 days. The surgical incisions of all patients were grade-A healing. Bone healing of glenoid fractures was observed three months after the operation. At the last follow-up, the shoulder range of motion was forward flexion 160.5°±9.3°, abduction 155.6°±12.5°, external rotation (neutral position) 40.7°±5.8°, internal rotation (neutral position) 65.4°±12.1°. The Constant-Murley score for the shoulder joint was (92.3±6.5) points (range 85-95), and the DASH score was (12.16±6.86) points (range 3.26 to 26.75).Conclusions:The axillary approach for Ideberg type I and II scapular glenoid fractures is a feasible surgical approach with complete access through the muscle gap, minimal surgical trauma, mild postoperative pain, and satisfactory clinical results.
Synthetically-charged Bose gas in the fast rotating regime
Authors: Abdulghani H. , Abbas A. H. , Ellithi A. , ElSherbini T h.M. , Hassan A. S. 
Published: March 2023

Abstract
We address the thermodynamic properties of a rotating Bose gas in a 3D space in the rapid rotation regime. In such a rotation regime, the 3D system has the shape of a flat pancake and shows exotic features that can never be found in the original system. Using the semi-classical approximation, the temperature dependence of the magnetization of rotating Bose gas is investigated. In the degenerate limit, the system does not show a Bose-Einstein condensation (BEC) phase transition at a definite transition temperature. However, it exhibits a large Landau diamagnetism at low temperatures, which diminishes as the speed of rotation decreases. Our findings are compared with the previous results.