bluuebunny/crossref_metadata_2025 huggingface dataset:
ChIP- based nuclear DNA isolation for genome sequencing in Pyropia to remove bacterial and cytosol DNA contamination
Authors: zhang zehao , Wang Junhao , Zhang Xiaoqian , Guan Xiaowei , Mao Yunxiang , Poetsch Ansgar , Wang Dongmei
Published: February 2023

Contamination from epiphytic bacteria and cytosolic DNA (plastid and mitochondrion) is challenging the accuracy of genome-wide analysis of nori-producing marine seaweed Pyropia yezoensis. Unlike bacteria and organellar DNA, Pyropia nuclear DNA is tightly associated with histone proteins. In this study, we applied Chromatin Immuno-precipitation (ChIP) of histone H3 to isolate nuclear DNA followed by high-throughput sequencing. More than 99.5% of ChIP-sequencing data are successfully aligned to the reference nuclear genome, remarkably higher than the ones from direct-extraction and nuclei-extraction data in which 40%-50% are from plastid. The proportion of data that mapped to the bacterial database when using ChIP extraction was very low. Additionally, ChIP-data can cover up to 89% of the nuclear genome, higher than direct-extraction data at equal data size and comparable to the latter at equal sequencing depth. The uncovered regions from the three methods are mostly overlapping, suggesting that incomplete sequencing accounts for the missing data, rather than failed chromatin-antibody binding in ChIP-extraction method. This ChIP-extraction method can successfully separate nuclear DNA from cytosolic DNA and bacterial DNA, thus overwhelmingly reducing the sequencing cost in genome resequencing project and provides a strictly purified reference data for genome assembly. The applicability to other macroalgae would makes it a valuable contribution to the algal research community.
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number variation confers glyphosate resistance in Eleusine indica
Authors: Zhang Chun , Johnson Nicholas , Hall Nathan , Tian Xingshan , Yu Qin , Patterson Eric
Published: February 2023

Genomic structural variation (SV) can have profound effects on an organism’s evolution, often serving as a novel source of genetic variation. Gene copy number variation (CNV), a specific form of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially to biotic and abiotic stresses. Resistance to the most widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important cosmopolitan grass, Eleusine indica (goosegrass); however, the origin and mechanisms of these resistance CNVs remain elusive in many weed species due to limited genetic and genomics resources. In order to study the target site CNV in goosegrass, we generated high-quality reference genomes for both glyphosate-susceptible and -resistant individuals, fine assembled the duplication of glyphosate's target site gene enolpyruvylshikimate-3-phosphate synthase (EPSPS), and revealed a novel rearrangement of EPSPS into the subtelomeric region of the chromosomes, ultimately leading to herbicide resistance evolution. This discovery adds to the limited knowledge of the importance of subtelomeres as rearrangement hotspots and novel variation generators as well as provides an example of yet another unique pathway for the formation of CNVs in plants.
Usefulness of mirtazapine and SSRIs in late-life depression. Post hoc analysis of the GUNDAM study.
Authors: Kato Masaki , Baba Hajime , Takekita Yoshiteru , Naito Minami , Koshikawa Yosuke , Bandou Hiroki , Kinoshita Toshihiko
Published: February 2023

Objective
Mirtazapine and SSRIs are widely prescribed as first-line agents for late-life depression. However, evidence for these drugs is mostly based on non-elderly patients. Therefore, we reanalyzed a randomized controlled trial of mirtazapine versus SSRIs for depression in a sub-population of late-life patients.
Methods
A randomized controlled trial was conducted with 141 patients, of whom 41 were elderly, and 100 were non-elderly. This study compared SSRIs and mirtazapine in late-life depression, examined late-onset and early adult-onset separately, and compared elderly and non-elderly patients for each drug. Treatment effects and adverse events were assessed using the Hamilton Depression Rating Scale and the Udvalg for Kliniske Undersøgelserside effect rating scale, respectively.
Results
In late-life depression, mirtazapine showed faster HAM-D total score improvement (3.3 points difference, p=0.021) and higher improvement in insomnia (1.7 points difference, p=0.001) and appetite (1.2 points difference, p=0.020). Similar findings were observed for late-onset depression with the HAM-D total score (4.3 points difference, p=0.007) and appetite (0.9 points difference, p=0.004), favoring mirtazapine. Depressive symptoms were generally less improved in late-life depression than in non-late-life depression. Regarding the effect of mirtazapine on appetite, late-life depression showed greater improvement (0.7 points difference, p=0.008). Nausea and micturition disturbances were more common with SSRIs in late-life depression than in non-late-lifedepression. In contrast, somnolence was less common in late-life depression with mirtazapine.
Conclusion
The potential usefulness of mirtazapine in elderly patients was demonstrated. The results also showed differences in the treatment response to SSRIs and mirtazapine between elderly and non-elderly patients.
Earthquake-induced soil landslides: volume estimates and uncertainties with the existing scaling exponents
Authors: Yunus Ali P. , Xinyu Chen , Catani Filippo , Subramaniam Srikrishnan Siva , Fan Xuanmei , Jie Dou , Sajinkumar K. S. , Gupta Ankita , Avtar Ram
Published: February 2023

Quantifying landslide volumes in earthquake affected areas is critical to understand the orogenic processes and their surface effects at different spatio-temporal scales. Here, we build an accurate scaling relationship to estimate the volume of soil landslides based on 1 m pre- and post-event LiDAR elevation models. On compiling an inventory of 1719 landslides in Mw 6.6 Hokkaido earthquake epicentral region, we find that the volume of soil landslides can be estimated by γ = 1.15–1.18. The total volume of eroded debris from Hokkaido catchments based on this new scaling relationship is estimated as 64–72 million m3. Uncertainties from the existing scaling relationships are found large except for the one found in recent literature 1. Based on the GNSS data approximation, we noticed that the co-seismic uplift volume is smaller than the eroded volume, suggesting that frequent large earthquakes may be counterbalancing the topographic uplift through erosion by landslides.
Identification of the pathogenic relationship between Long COVID and Alzheimer's disease by bioinformatics methods
Authors: Ren Hui , Chen Liang-Liang , Liang Fengjun , Ding Tianhong , Zhang Running , Wei Peifeng , Miao Feng
Published: February 2023

Background
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an unprecedented global health crisis. Although many Corona Virus Disease 2019 (COVID-19) patients have recovered, the long-term consequences of SARS-CoV-2 infection are unclear. Several independent epidemiological surveys and clinical studies have found that SARS-CoV-2 infection and Long COVID are closely related to Alzheimer's disease (AD). This could lead to long-term medical challenges and social burdens following this health crisis. However, the mechanism between Long COVID and AD is unknown.
Methods
Genes associated with Long COVID were collected from the database. Two sets of AD-related clinical sample datasets were collected in the Gene Expression Omnibus (GEO) database by limiting screening conditions. After identifying the differentially expressed genes (DEGs) of AD, the significant overlapping genes of AD and Long COVID were obtained by taking the intersection. Then, four kinds of analyses were performed, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analysis, protein-protein interaction (PPI) analysis, identification of hub genes, hub gene verification and transcription factors (TFs) prediction.
Results
A total of 197 common genes were selected for subsequent analysis. GO and KEGG enrichment analysis showed that these genes were mainly enriched in multiple neurodegenerative disease related pathways. In addition, 20 important hub genes were identified using cytoHubba. At the same time, these hub genes were verified in another data set, where 19 hub gene expressions were significantly different in the two diseases and 6 hub genes were significantly different in AD patients of different genders. Finally, we collected 9 TFs that may regulate the expression of these hub genes in the Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRUSST) database and verified them in the current data set.
Conclusion
This work reveals the common pathways and hub genes of AD and Long COVID, providing new ideas for the pathogenic relationship between these two diseases and further mechanism research.
Preliminary Investigation Into Prospective Applications of Nanosilver, Produced Using Teff (Eragostris Tef) Flour Extract
Authors: KONWARH ROCKTOTPAL , Workie Abie , Moges Abyalew , Seifu Daniel , Elias Dereje , Kebede Nahil , Tsigemariam Yosef , Singh Anand Pratap
Published: February 2023

Silver-based nanomaterials have etched an indelible mark in multiple domains. The green synthesis of silver nanoparticles has received significant attention in comparison to the conventional use of toxic chemicals and reagents in the preparatory stages. In this milieu, the work reported here highlights the use of an aqueous extract of teff (Eragostris tef) flour to prepare silver nanoparticles (TSNPs). The compositional abundance of various phytochemicals, sunlight-induced bio-reduction of silver ions, and subsequent stabilization of the nanostructures by teff’s biomolecules were adroitly exploited. UV-visible spectroscopic analysis was employed to track the evolution of the TSNPs over time and their month-long storage stability. Exhibiting λmax at around 426 nm and energy gap (as revealed by Tauc’s plot) of 2.26 eV, the silver nanomaterial was employed for methylene blue dye degradation (50% degradation in less than 50 min) and DPPH scavenging (IC50 = 243.42 μL containing 410 μg of TSNPs), attesting their catalytic and anti-oxidant potency. On the other hand, anticoagulant action and a concentration-dependent variation were noted for radicle length post germination of Cicer arientinum seeds, treated with the TSNPs. The TSNPs could have profound implications in multiple domains.
Mometasone furoate inhibits the progression of head and neck squamous cell carcinoma via regulating PTPN11
Authors: Qiu Lin , Gao Qian , Tao Anqi , Jiang Jiuhui , Li Cuiying
Published: February 2023

Background: Mometasone Furoate (MF) is a kind of glucocorticoid with extensive pharmacological action including inhibiting tumor progression, however, the role of MF in head and neck squamous cell carcinoma (HNSCC) was still unclear. This study was aim to evaluate the inhibitory effect of MF against HNSCC and investigate the underlying mechanism.
Methods: Cell viability, colony formation, cell cycle and cell apoptosis were detected to explore the effect of MF on HNSCC cells. Xenograft study model was conducted to investigate the effect of MF on HNSCC in vivo. The core target of MF against HNSCC was identified by network pharmacology analysis, TCGA database analysis and real-time PCR. Molecular docking was performed to detect the binding energy. Protein tyrosine phosphatase non-receptor type 11 (PTPN11) overexpressed cells were constructed and then cell viability and the expression levels of proliferation- and apoptosis-related proteins were detected after treated with MF to explore the role of PTPN11 in the inhibitory of MF against HNSCC.
Results: After cells treated with MF, cell viability and the number of colonies were decreased, cell cycle was arrested and cell apoptosis was increased. Xenograft study results showed that MF could inhibit cell proliferation via promoting cell apoptosis in vivo. PTPN11 was the core target of MF against HNSCC via network pharmacology analysis, TCGA database analysis and real-time PCR. Molecular docking results revealed PTPN11 exhibited the strongest binding ability to MF. Finally, MF could attenuate the effect of increased cell viability and decreased cell apoptosis caused by PTPN11 overexpression, suggesting that MF could inhibit the progression of HNSCC by regulating PTPN11.
Conclusion: MF targeted PTPN11 to promote cycle arrest and cell apoptosis subsequently performed an effective anti-tumor activity.
Impact of H9N2 Infection on the Pathological and Immunological Effects of the IBD Vaccine in Chicks: A Study of Vaccine Interaction and Immune Response
Authors: Khalil N. W. , Elshorbagy M. A. , Elboraay E. M. , Helal A. M.
Published: February 2023

Background:
This study aimed to investigate the impact of H9N2 infection on the pathological and immunological effects of the IBD vaccine, and how their interaction affects the immune response to other vaccines. The objective was to determine if H9N2 infection before IBD vaccination influences the efficacy of the vaccine and if it impacts other vaccines' immune response. One hundred SPF chicks were divided into four groups in four isolators that were either H9N2 challenged, IBD vaccinated, both, or neither. Blood samples were collected weekly to measure antibody titers against IBDV, ND, H5, and H9. Cloacal swabs were taken on the 4th and 8th days post-vaccination to quantify the IBD vaccine shedding. Five chicks per group were euthanized at the 17th, 21st, and 25th days old to calculate immune organ indices and conduct histopathological examinations.
Results:
The study's results revealed that pre-challenge with H9N2 affected many factors. The dual-treated group had a significant decrease in the bursal index compared to the other groups. The bursal microscopical score and renal lesion score of the dual-treated group recorded a significant rise when compared to the other groups. The shedding of the IBD vaccine was negatively affected by pre-infection with H9N2, so the dual-treated group recorded a significant decrease in IBDV shedding in comparison to the IBD-vaccinated group. Additionally, the immune response against the IBD vaccine significantly decreased in the dual-treated group. Finally, there was an increase in the immunosuppressive effect of the IBD vaccine, which reflected a significant decline in the antibody titers against ND and H5 in the dual-treated group.
Conclusion:
The study suggests that early diagnosis of H9N2 before IBD vaccination is crucial. Pre-challenge with H9N2 significantly impacted the pathological and immunological effects of the IBD vaccine. The results showed a decrease in IBD vaccine shedding and immune response against the IBD vaccine in the dual-treated group. The immunosuppressive effect of the IBD vaccine also affected the immune response to other vaccines, as shown by the significant decline in the antibody titers against ND and H5 in the dual-treated group. Therefore, the study highlights the importance of considering H9N2 infection status before administering the IBD vaccine to ensure optimal immune response and protection.
Modularized and Scalable Compilation for Double Quantum Dot Quatum Computing
Authors: He Run-Hong , Xu Xu-Sheng , Byrd Mark , Wang Zhao-Ming
Published: February 2023

Any quantum program on a realistic quantum device must be compiled into an executable form while taking into account the underlying hardware constraints. Stringent restrictions on architecture and control imposed by physical platforms make this very challenging. In this paper, based on the quantum variational algorithm, we propose a novel scheme to train an Ansatz circuit and realize high-fidelity compilation of a set of universal quantum gates for singlet-triplet qubits in semiconductor double quantum dots, a fairly heavily constrained system. Furthermore, we propose a scalable architecture for a modular implementation ofquantum programs in this constrained systems and validate its performance with two representative demonstrations, Grover's algorithm for the database searching (static compilation) and a variant of variational quantum eigensolver for the Max-Cut optimization (dynamic compilation). Our methods are potentially applicable to a wide range of physical devices. This work constitutes an important stepping-stone for exploiting the potential for advanced and complicated quantum algorithms on near-term devices.
Echo2Pheno: A deep learning application to uncover echocardiographic phenotypes in conscious mice
Authors: Bukas Christina , Galter Isabella , Silva-Buttkus Patricia , Fuchs Helmut , Maier Holger , Gailus-Durner Valerie , Müller Christian L. , Angelis Martin Hrabě , Piraud Marie , Spielmann Nadine
Published: February 2023

Echocardiography, a rapid and cost-effective imaging technique, assesses cardiac function and structure. Despite its popularity in cardiovascular medicine and clinical research, image-derived phenotypic measurements are manually performed, requiring expert knowledge and training. Notwithstanding great progress in deep learning applications in small animal echocardiography, the focus has so far only been on images of anaesthetized rodents. We present here a new algorithm specifically designed for echocardiograms acquired in conscious mice called Echo2Pheno, an automatic statistical learning workflow for analyzing and interpreting high-throughput non-anesthetized transthoracic murine echocardiographic images in the presence of genetic knockouts. Echo2Pheno comprises a neural network module for echocardiographic image analysis and phenotypic measurements, including a statistical hypothesis-testing framework for assessing phenotypic differences between populations. Using 2159 images on 16 different knockout mouse strains of the German Mouse Clinic, Echo2Pheno accurately confirms known cardiovascular genotype–phenotype relationships (e.g. Dystrophin) and discovers novel genes (e.g. CCR4-NOT transcription complex subunit 6-like, Cnot6l, and synaptotagmin-like protein 4, Sytl4), which cause altered cardiovascular phenotypes, as verified by H&E-stained histological images. Echo2Pheno provides an important step toward automatic end-to-end learning for linking echocardiographic readouts to cardiovascular phenotypes of interest in conscious mice.
Quick insights into whisky – investigating rapid and efficient methods for sensory evaluation and chemical analysis
Authors: Haug Helen , Grasskamp Andreas T. , Singh Satnam , Strube Andrea , Sauerwald Tilman
Published: February 2023

The evaluation of aroma properties of beverages both analytically as well as with human sensory is a challenging task and most often related to time- and cost-intensive analyses. Whisky is a spirit offering a wide variety of aroma impressions caused by a complex mixture of aroma active compounds. In the present study, methods for the efficient evaluation of aroma characteristics are evaluated for 16 whisky samples of different origins (Scotch and American). Rate all that apply (RATA) was applied as a rapid sensory method for the sensory evaluation of whiskies. Sensory evaluation of the samples led to the determination of eight significant aroma attributes: Caramel / cream caramel / toffee, vanilla, (canned) peach, phenolic, smoky, fruity, flowery and (fermented) apple / cider. Chemical analysis was conducted by stir bar sorptive extraction (SBSE) coupled to gas chromatography mass spectrometry in combination with an in-house data processing tool for automated analyte identification. Through chemical analysis of the whisky samples and automated compound identification, over 200 mostly aroma-active volatiles were detected. To test both approaches for their potential for sample classification, a simple classification problem (Scotch vs. American) was applied. Linear discriminant analysis (LDA) indicates both that sensory evaluation by RATA (97.86%) and the applied analytical procedure (96.94%) are suitable for the distinction between the two whisky types. For both approaches, markers were identified for the classification. These investigations build a solid foundation for the implementation of a versatile platform for rapid and efficient aroma evaluation for various foodstuffs and beverages.
Contribution Of Hydrogeochemical And Statistic Tools To The Acquisition Of Water Quality In The North-Eastern Of Algeria: Annaba-El Tarf
Authors: BOUNAB Samia , SEDRATI Nassima , KHEMMOUDJ Kaddour , MAJOUR Habiba
Published: February 2023

This work was conducted on 34 samples spread over 4 areas (Bouteldja, El Tarf, Les Salines et Barrahal) tapping the shallow and deep aquifer of groundwater in the North-eastern Algeria (Annaba-El Tarf), one sampling campaign was conducted in 2017 to describe the chemistry of the water and its interaction with the rock. The interpretation of the geological-geophysical and hydrogeological data allowed us to highlight two principal aquifers. The first consists of the sandy clay formations up to 18 m thick. It is generally free except at a few points where it is captive under clay levels. The second is more important localized in the gravel layer below first aquifer; it covers the entire study area. It is formed by Plio-Quaternary gravels, sands and pebbles and is contained in the collapse basin. The methodology used for the processing of the analysis results is based on multivariate statistical methods and characteristic ratios coupled with hydrochemical methods, as well as the calculation of saturation indices. The results show that the water quality is controlled both by the dissolution of the minerals of the evaporite formations and those of the carbonate formations, alteration of silicates and marine invasion.
Multiple antiplatelet therapy in ischemic stroke already on antiplatelet agents
Authors: Kim Tae Jung , Lee Ji Sung , Yoon Jae Sun , Park Soo-Hyun , Oh Mi Sun , Jung Keun-Hwa , Yu Kyung-Ho , Lee Byung-Chul , Ko Sang-Bae , Yoon Byung-Woo
Published: February 2023

Background: Optimal antiplatelet strategy for patients with ischemic stroke who were already on single antiplatelet therapy (SAPT) remains to be elucidated. This study aimed to evaluate the effect of different antiplatelet regimens on vascular and safety outcomes at 1 year after non-cardioembolic stroke in patients previously on SAPT.
Methods: We identified 9,284 patients with acute non-cardioembolic ischemic stroke that occurred on SAPT using linked data. Patients were categorized into three groups according to antiplatelet strategy at discharge: 1) SAPT, 2) dual antiplatelet therapy (DAPT), and 3) triple antiplatelet therapy (TAPT). One-year outcomes included recurrent ischemic stroke, composite outcomes (recurrent ischemic stroke, myocardial infarction, intracerebral hemorrhage, and death), and major bleeding.
Results: Of 9,284 patients, 5,565 (59.9%) maintained SAPT, 3,638 (39.2%) were treated with DAPT, and 81 (0.9%) were treated with TAPT. Multiple antiplatelet therapy did not reduce the risks of 1-year recurrent stroke (DAPT, hazard ratio [HR] 1.08 [95%confidence interval, CI, 0.92–1.27], P= 0.339; TAPT, HR, 0.71 [95%CI, 0.27–1.91], P = 0.500) and 1-year composite outcome (DAPT, HR, 1.09 [95%CI, 0.68–1.97], P = 0.592; TAPT HR, 1.46 [95%CI, 0.68–1.97], P = 0.592). However, the TAPT groups showed an increased risk of major bleeding complications (DAPT, HR, 1.23 [95%CI, 0.89–1.71], P = 0.208; TAPT, HR, 4.65 [95%CI, 2.01–10.74], P < 0.001).
Conclusions: Additional use of antiplatelet agents in patients with non-cardioembolic ischemic stroke who were already on SAPT did not reduce the 1-year incidence of vascular outcomes, although it increased the risk of bleeding complications.
Immunotherapy with cure potential of multi-drug resistant hematologic malignancies using IL-2 preactivated intentionally mismatched donor lymphocytes
Authors: Slavin Shimon
Published: February 2023

Purpose: Unfortunately, cure of multi-drug resistant (MDR) hematologic malignancies remains an unmet need. Donor lymphocyte infusion (DLI) following allogeneic stem cell transplantation (SCT) can sometimes eliminate multi-drug resistant leukemia but at a risk of acute and chronic graft-vs-host disease (GVHD) and procedure-related toxicity. Supported by pre-clinical experiments in animal models, we hypothesized that immunotherapy induced by non-engrafting intentionally mismatched IL-2 activated killers (IMAK) including both T & NK cells could induce safer, faster and much more effective immunotherapy while avoiding the need for SCT and the risks of GVHD.
Methods: IMAK treatment was applied in 33 patients with MDR hematologic malignancies conditioned with cyclophosphamide 1,000mg/m^2 based protocol. Haploidentical or unrelated donor lymphocytes were preactivated with IL-2 6,000 IU/ml for 4 days. IMAK was combined with Rituximab in 12/23 patients with CD20+ B cells.
Results: A total of 23/33 patients with MDR (4 failing SCT) achieved complete remission (CR).
First patient currently 30 years with no further treatment and 5 observed for >5 years (2 AML; 2 multiple myeloma, 1 ALL & 1 NHL) can be considered cured. No patient developed >grade 3 toxicity or GVHD. No residual male cells were detectable among 6 females treated with male cells beyond day +6, confirming that GVHD was prevented by consistent early rejection of donor lymphocytes.
Conclusions: We hypothesize that safe and superior immunotherapy of MDR with cure potential may be accomplished by IMAK, most probably in patients with low tumor burden, but that remains to be confirmed by future clinical trials.
The Experimental Design Approach to Removal of Endocrine Disrupting Compounds from Domestic Wastewater by Electrooxidation Process
Authors: SÖZÜDOĞRU Onur , KOÇOĞLU Elif Seda , YILMAZ Alper Erdem , BAKIRDERE Sezgin , KOMESLİ Okan Tarık
Published: February 2023

In this study, the treatment performance of the process in the removal of Endocrine Disrupting Compounds (EDCs) from domestic wastewater by a laboratory-scale electrooxidation process using Ti/IrO₂/RuO₂ electrodes as an anode was evaluated using response surface method (RSM). The effect of pH, current density, and flow rate on the electrochemical treatment of 17α-ethinylestradiol, β-estradiol, triclosan, and estrone, which are often present in wastewater, has been studied. Using Box-Behnken Design (BBD), the parameters influencing the removal efficiencies were optimized for the Electrooxidation process (EOP), and the models created essential second-order quadratic models for the EOP process. The Response Surface Method yielded results that reasonably agreed with the measured values. The maximum removals of triclosan, 17α-ethinylestradiol, and β-estradiol were attained at 92,90%, 97,76%, and 95,36% respectively, under experimental conditions optimized pH= 3,68, current density= 20 A and flow rate= 8,83 mL/min for EOP. Removal efficiencies have achieved their maximum levels at low pH, high current density, and low flow rate. At the same time, the electrooxidation method could not completely remove the estrone.
Synthesis and Characteristics of Graphene-Graphene Oxide Material Obtained by an Underwater Impulse Direct Current Discharge
Authors: Sirotkin Nikolay , Korolev Viktor
Published: February 2023

This work proposed a novel approach, in which an impulse underwater discharge was used to produce graphene-graphene oxide material in distilled water. The characteristics of this discharge were presented, including electrical parameters, plasma composition, and electron concentration. Graphene-based material produced using this approach can be evenly dispersed in water without the use of a surfactant or stabilizer, and is suitable for storage at room temperature. Ultraviolet–visible spectroscopy was employed to analyze the optical properties of the graphene-based structures. Scanning electron microscopy was adopted to explore the morphology and size of the particles. The FTIR spectroscopy confirms the formation of graphene oxide. The Raman spectroscopy demonstrates the formation of a graphene-containing multilayer material. The results of this study confirmed that graphene-based material production by impulse underwater discharge is a low-cost, fast, and effective manufacturing method.
Incidence and clinical relevance of postoperative diarrhea after minimally invasive gastrectomy for gastric cancer: A single institution retrospective study of 1476 patients
Authors: Fujita Masahiro , Nakauchi Masaya , Suzuki Kazumitsu , Serizawa Akiko , Akimoto Shingo , Tanaka Tsuyoshi , Shibasaki Susumu , Inaba Kazuki , Tochio Takumi , Hirooka Yoshiki , Uyama Ichiro , Suda Koichi
Published: February 2023

Purpose
Postoperative diarrhea (PD) remains one of the significant complications. Only a few studies focused on PD after minimally invasive surgery. We aimed to investigate PD after minimally invasive gastrectomy for gastric cancer.
Methods
A total of 1476 consecutive patients with gastric cancer undergoing laparoscopic or robotic gastrectomy between 2009 and 2019 at our institution were retrospectively reviewed. PD was defined as continuous diarrhea for ≥ 2 days, positive stool culture, or positive clostridial antigen test. The incidence, causes, and related clinical factors were analyzed.
Results
Of the 1476 patients, the median age was 69 years. Laparoscopic and robotic approaches were performed in 1072 (72.6%) and 404 (27.4%), respectively. Postoperative complications with Clavien–Dindo classification grade of ≥ IIIa occurred in 108 (7.4%) patients. PD occurred in 89 (6.0%) patients. Of the 89 patients with PD, Clostridium difficile, enteropathogenic Escherichia coli, and methicillin-resistant Staphylococcus aureus were detected in 24 (27.0%), 16 (33.3%), and 7 (14.6%) patients, respectively. Multivariate analysis revealed that age ≥ 75 years (OR 1.62, 95% CI [1.02–2.60], p = 0.042) and postoperative complications (OR 6.04, 95% CI [3.54–10.32], p < 0.001) were independent risk factors for PD. In patients without complications, TG (OR 1.88) and age of ≥ 75 years(OR 1.71) were determined as independent risk factors.
Conclusion
The incidence of PD following minimally invasive gastrectomy for gastric cancer was 6.0%. Older age and TG were obvious risk factors in such a surgery, with the latter being a significant risk even in the absence of complications.
An adaptive spatio-temporal neural network for PM2.5 concentration forecasting
Authors: Zhang Xiaoxia , Li Qixiong , Dong Liang
Published: February 2023

The prediction of PM2.5 concentration is essential and important for improving people's physical and mental health, as one of the main sources of air pollution, it limits the sustainable development of urban areas. In this paper, we propose a hybrid prediction model to predict PM$_{2.5}$ concentration for the next 72 hours by employing the spatio-temporal information of monitoring stations, called adaptive spatio-temporal prediction network (ASTP-NET), which consists of four components: feature extraction module, spatial attention module, Multi-Layer Bi-LSTM and future time features. The feature extraction module conducts adaptive feature extraction while preserving the inherent spatio-temporal features of different stations. The spatial attention network aims to obtain the spatial attention weights of the auxiliary and target stations based on the target station features. Multi-Layer Bi-LSTM with the transformation mechanism is executed to capture the entangled temporal features of all stations from their weighting fusion features. The purpose of adding future time feature module is to enhance the prediction performance through incorporating prior knowledge and expanding the time perception horizon. The evaluation of ASTP-NET is implemented based on the air quality dataset of Xi'an and the results show our model outperforms other latest state-of-the-art methods. The methodology can be applied to predict multivariate time series data in different domains.
Implications of additive x additive epistasis for common bean breeding
Authors: de Melo Rita Carolina , Coimbra Jefferson Luís Meirelles , Silva João Gilberto Corrêa da , Cerutti Paulo Henrique , Carbonari Luan Tiago dos Santos , Guidolin Altamir Frederico
Published: February 2023

The presence of epistasis in complex traits can be significant and affect the selection of segregating populations undesirably. The purpose of this study was to determine the epistatic genetic components that influence root and shoot traits of common bean and identify their effect on the performance of segregating populations. The field experiment consisted of 49 treatments (backcross progenies, parents and segregating populations in the F2and F3generations). The cross P1-BAF53 (Andean) x P2-IPR 88 Uirapuru (Mesoamerican) as reference. Six traits were taken into consideration: root distribution (%), first pod length (cm), number of grains (plot), plant height (cm), reproductive cycle (days) and number of basal branches (plot). Additive x additive epistasis significantly affected 50% of the above traits. For root distribution (RD), this genetic component deteriorated the mean performance of the progenies in relation to the parents, regardless of the presence of dominance deviations and additive x dominant and dominant x dominant epistasis. In addition, lower variation in the different generations (parents and F2and F3progenies) was found for RD than for the other traits. Rather, no additive x additive interaction component for plant height was detected, but predominance of genetic deviations of dominance and transgressive segregation events were identified. Thus, additive x additive epistasis can hamper the success of a breeding program, for being associated with low-variability traits. This fact may be related with the number of crosses and/or the choice of genetically more distant parents for the program, and possibly with the presence of linked genes.
Climate change perceptions of shifting cultivators vis-a-vis meteorological observations influencing their adaptation decisions in the north-eastern region of India
Authors: Paul Sudipta , Chakraborty Debasish , Padaria Rabindra , Tripathi Anil Kumar
Published: February 2023

Climate change has become a reality and the agriculture sector is directly confronted by its ill effects. The poor dwellers of hilly tracts of the north-eastern region of India are totally dependent on rainfed agriculture practicing shifting cultivation, the most primitive way of crop cultivation in the history of humankind which is still practiced by 240 million indigenous people of the world. The present study is aimed to integrate local perspectives on the global phenomenon of climate change as we compare shifting cultivators’ (n = 600) climate change perceptions with meteorological data for a holistic understanding of adaptation decisions in shifting cultivation. Climatic trends are analyzed from the precipitation and temperature data of the India Meteorological Department. Study results show that shifting cultivators’ climate change perceptions align well with climatic trends for temperature-related events though some inconsistencies exist for precipitation events. Further, the significance and strength of the association between shifting cultivators’ climate change perceptions and their adaptation decisions are statistically tested by Chi-square and Cramer’s V respectively. Results reveal that three-fourths (~ 76%) of the respondents made alterations in the shifting cultivation calendar as an adaptation strategy to climate change. Adaptation decisions pertaining to the sowing and post-sowing activities (weed control, crop protection, and harvesting) are more strongly associated with climate change perception compared to pre-sowing activities (selection and clearing of forested hilly lands). This study identifies the appropriateness of the climate change perceptions of shifting cultivators and recommends their inclusion for the effective formulation of policies regarding climate risk management.
Spatial and Sexual Divergence of Gut Microbial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae)
Authors: Hirata Kazuya , Asahi Toru , Kataoka Kosuke
Published: February 2023

The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut region, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut microbiota of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by gut region rather than sex. In the species richness and diversity analyses, there were large differences among the gut regions, but only minor differences between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism, and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the compartment-dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.
Increasing atmospheric dryness reduces boreal forest tree growth
Authors: Mirabel Ariane , Girardin Martin P. , Metsaranta Juha , Way Danielle , Reich Peter B
Published: February 2023

Rising atmospheric vapor pressure deficit (VPD) associated with climate change impacts tree growth and carbon storage through its effects on stomatal closure, evapotranspiration, and soil dryness. However, ground truth analyses of the effects of changing VPD on forest growth remain limited to focal species and areas. We assessed the response of Canada’s boreal forests to VPD changes during 1951-2018 using a tree-growth increment network with 5,000 species-site combinations. Roughly half of the sites showed a relationship between growth and VPD, with the most common response being a negative relationship between previous year VPD and current year growth, while current year VPD also tended to reduce growth. Species, tree age and soil moisture were primary determinants of tree VPD responses, with younger trees and key species like Picea glauca and Populus tremuloides showing higher VPD sensitivity. Since 1951, increases in summer VPD in Canada have paralleled growth decreases, particularly in spruce species.
Green Infrastructure in ecosystem provisions: Macro to Micro
Authors: saba Bushra
Published: February 2023

The paper delves into the provision of green spaces and their contribution to forming a liveable and sustainable green city. It studies the natural cover of the city as a whole in comparison to the availability of green infrastructure in the wards of the Bhopal urban area. Analysis reveals the green percentage reduction from 44% in 1990 to 21% in 2022. Furthermore, the ward-level green cover is found to be less towards the city center in contrast to newer peripheral wards of the city. Of all the wards, 18% wards lie under dense cover, 69% wards with a moderate green cover and 13% wards with the least green cover. The research portrays the ecosystem services by the available green cover in the city region with a micro-level proposal towards retaining the natural canvas of the city.
Influence of human behavior on COVID-19 based on reaction diffusion equations
Authors: Zhi Shun , Niu Hongtao , Su You-hui , Han Xiaoling
Published: February 2023

COVID-19 is a highly infectious disease spreading through human droplets and contact. To investigate the effect of human behavior changes on the spread of COVID-19, a reaction-diffusion model that contains contact rate functions related to human behavior is studied. The basic reproduction number $\mathcal{R}_{0}$ for this system is derived and a threshold-type result on its global dynamics in terms of $\mathcal{R}_{0}$ is established in this paper. More precisely, we show that the disease-free equilibrium is globally asymptotically stableif $\mathcal{R}_{0}\leq1,$ and the system admits a positive solution and the disease is uniformly persistent if $\mathcal{R}_{0}>1$. By the numerical simulations of the analytic results, we find that human behavior changes may lower infection levels and reduce the number of exposed and infected humans.
Use of the Plastic Garbage Bag in Replacing a Prolapsed Uterus
Authors: Newman William
Published: February 2023

Prolapsed uterus replacement is usually just a hard and messy job and it hasn't changed a whole lot from the way our predecessors in the profession did it many years ago. Two items that I use, and one of them is not labeled in the topic, are a plastic garbage bag or a cadaver bag (I actually use a Haver-Lockhart cadaver bag, but a large plastic garbage bag works the same) and the other one is a stool and we just call it a dove hunter stool.
Epidemiology of Neospora Infection in Ontario Holstein Dairy Cows
Authors: Duffield T. , Peregrine A. , McEwen B. , Hietala S.
Published: February 2023

This data provides some insight into the epidemiology of Neospora seropositivity in Ontario dairy herds. In addition, it appears that cows infected with Neospora caninum based on serology have an increased risk for retained placenta at calving.
Rethinking Coliform Vaccine Programs
Authors: Burton J. L. , Erskine R. J.
Published: February 2023

Core-antigen vaccine technology has been available for the prevention of coliform mastitis for over ten years. However, unresolved issues regarding the most effective method to incorporate this technology into a dairy herd health program remain. These include number of vaccinations, effect of vaccinations on milk production of cows, and if risk factors associated with the incidence of clinical coliform mastitis correlate to vaccination schedules. This paper will discuss the immunological justification and limitations of vaccination protocols for coliform mastitis, and propose applications of this information.
Low Mycobacterium avium subspecies paratuberculosis ELISA Specificity in a Dairy Herd
Authors: Grooms Daniel L. , Durst Phil , Kaneene John B.
Published: February 2023

Johne's Disease (JD) is an important infectious disease of cattle caused by Mycobacterium avium subspecies paratuberculosis (MAP). It is estimated that over 50% of US dairy herds are infected with MAP. Current JD diagnostic tests detect either an immune response to MAP or the actual organism in feces or tissues. The JD ELISA detects antibodies to MAP and is the most common assay used to detect an MAP immune response. Because of the pathogenesis of JD, the sensitivity of the JD ELISA is reported to be less than 50% when used to detect JD infected adult cattle. The specificity of the JD ELISA is reported to be greater than 90%. However, the assay specificity may vary significantly between herds. In this case study, low MAP ELISA specificity in an individual dairy herd is described.
Efficacy of Tulathromycin and Oxytetracycline on Reducing the Incidence of Otitis Media Caused by Mycoplasma bovis in Preweaned Holstein Dairy Calves
Authors: Sockett D. C. , Jicinsky S. A. , Earleywine T. J. , Miller B. L. , Johnson T. E. , Olson J. D.
Published: February 2023

The Land O'Lakes Research facility in Webster City, IA conducts trials on three- to five-day-old Holstein bull calves purchased from sales barns located in Wisconsin. Calves are sold to producers after completion of the research trials. During the past seven years, Mycoplasma bovis has reduced the value and number of saleable calves primarily due to otitis media and subclinical pneumonia. To better understand the transmission dynamics of M. bovis and the potential therapeutic benefit of prophylactic antimicrobial drugs, a study was initiated to evaluate calf growth, health, treatment costs and isolation rate of M. bovis from the pharynx of calves housed at the facility.
Vaccination with Streptococcus uberis Adhesion Molecule Induces Isotypic Antibody Responses in Bovine Serum and Colostrum
Authors: Prado M. E. , Luther D. A. , Lewis M. J. , Headrick S. I. , Almeida R. A. , Oliver S. P.
Published: February 2023

Despite implementation of mastitis control practices that have significantly reduced the incidence of contagious mastitis, recent studies have shown that as the prevalence of contagious mastitis pathogens decreased, the incidence of environmental mastitis pathogens increased. Streptococcus uberis is one of the most commonly isolated environmental pathogens, infecting mammary glands when conditions are favorable. During the last decade, our research efforts have concentrated on understanding the mechanisms utilized by S. uberis to invade the mammary gland. Using in vitro models we have identified and partially characterized S. uberis adhesion molecule (SUAM). We demonstrated that SUAM was involved in adherence to, internalization into, and persistence of S. uberis in bovine mammary epithelial cells and may be an excellent target for vaccine development. The objective of this study was to evaluate isotypic antibody responses of cattle vaccinated with recombinant SUAM (rSUAM) in serum and colostrum.
Bulk Tank Raw Milk Quality
Authors: Keefe Greg , ElMoslemany Ahmed
Published: February 2023

Raw bulk tank milk (BTM) quality (SCC and bacteria burden) is used to quantify the health and safety of milk. Laboratory-based studies have demonstrated that milk with lower bacteria and somatic cell count produces milk products with superior quality attributes and shelf-life. Raw BTM is subjected to a number of tests to indicate udder health, milk harvest hygiene and storage conditions on the farm. These tests include; total bacterial count (TBC) (or standard plate count (SPC)), preliminary incubation count (PIC), laboratory pasteurization count (LPC) and coliform count (CC), as well as SCC. The objective of this study was to examine the relationship between raw BTM quality and consumer experience with fluid milk products and to survey on-farm risk factors for bacterial milk quality.
Incidence Risk Patterns of Intramammary Infection Pathogens during the Dry Period in Holstein Dairy Cattle
Authors: Calloway C. D. , Dohoo I. R. , Keefe G. P.
Published: February 2023

Intramammary infections acquired during the dry period are difficult to diagnosis and tend to lead to decreased production in the subsequent lactation. In addition, the use of dry cow therapies have virtually eliminated major pathogens, such as Streptococcus agalactiae. However, use of dry cow therapy or teat sealants may have questionable efficacy against other pathogens. Selective dry cow therapy, based on farm- or cow-specific pathogen profiles, tend to decrease usage of antimicrobial products. However, to generate farm-specific pathogen profiles, knowledge of incidence of intramammary pathogens is needed. The objective of this observational study is to determine the incidence of intramammary pathogens in dairy cattle across the dry period.
Observational Study of Blood Glucose, Non-Esterified Fatty Acid, and Beta-Hydroxybutyrate Concentrations in a Commercial Dairy Herd with a High Incidence of Ketosis
Authors: Calderon D. F. , Cook N. B. , Oetzel G. R.
Published: February 2023

Ketosis, defined as blood beta-hydroxybutyrate (BHBA) concentrations greater than 1,400 umol/1, is an important problem in dairy herds. Ketosis in early lactation has been associated with decreased milk yield, increased risk for displaced abomasum, and impaired reproductive performance. The objective of this study was to investigate relationships between concentrations of blood BHBA, glucose, and non-esterified fatty acids (NEFA) in transition dairy cows in a commercial dairy herd with a high incidence of ketosis.