bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impaired cellulose decomposition in a headwater stream receiving subsurface agricultural drainage
Authors: Poisson Rebecca , Yates Adam G. 
Published: September 2022

Abstract
Background
Agricultural development of former wetlands has resulted in many headwater streams being sourced by subsurface agricultural drainage systems. Subsurface drainage inputs can significantly influence stream environmental conditions, such as temperature, hydrology, and water chemistry, that drive ecological function. However, ecological assessments of subsurface drainage impacts are rare. We assessed the impact of an agricultural drainage system on cellulose decomposition and benthic respiration using a paired stream study in a headwater branch of Nissouri Creek, in Ontario, Canada. Adjacent first order segments sourced by a spring-fed marsh and a cropped field with subsurface drainage, as well as the adjoining trunk segment, were sampled over a year using the cotton strip assay to measure cellulose decomposition and benthic respiration.

Results
Assessments of cellulose decomposition revealed a one-third reduction in the drainage-sourced segment compared to marsh-sourced segment. Between segment differences in cellulose decomposition were associated with reduced summer temperatures in the drainage-sourced segment. Impacts of stream cooling from the drainage-sourced segment were transmitted downstream as cellulose decomposition was slower than expected throughout the drainage-sourced segment and for several hundred meters down the adjoining trunk segment. Benthic respiration only differed between the drainage- and marsh-sourced segments in spring, when stream temperatures were similar.

Conclusions
Our findings suggest there may be a widespread reduction in cellulose decomposition in streams across similar agricultural regions where subsurface drainage is prevalent. However, cooling of streams receiving significant amounts of water inputs from subsurface drainage systems may impart increased resiliency to future climate warming.
Selective biomarkers for inflammation and infection are associated with post-operative complications following transperineal template prostate biopsy (TTPB): a single-centre observational clinical pilot-study
Authors: Snyper Nana Yaa Frempomaa , Pike Joanne , Ekwueme Kingsley , Shergill Iqbal , Hughes Stephen Fôn 
Published: September 2022

Abstract
Background
Prostate cancer (PCa) and benign prostatic hyperplasia (BPH) are the most common prostate disorders in the UK, which cause considerable ill health in older men. Transperineal template prostate biopsy (TTPB) has emerged as a reliable procedure for the histopathological diagnosis of PCa and BPH due to its higher cancer detection rates. Although antiseptic preparation and antibiotic prophylaxis are used to ensure safety in patients undergoing surgical intervention, post-operative complications, such as infection and bleeding are still unavoidable, resulting in re-admissions, with resource implications. Currently, there is no biomarker profile to predict outcomes or monitor patients during the post-operative course. The main aim of this single-centre observational clinical pilot-study was to investigate the role of inflammatory and infection biomarkers following TTPB and their association with post-operative complications.

Methods
Forty-five patients scheduled for elective TTPB were recruited after informed consent at the Wrexham Maelor and Glan Clwyd Hospitals, North Wales, UK (n = 45). Prior to surgery, venous blood samples were collected at baseline and subsequently at 30, 120, and 240 min post-operatively. Urine samples were collected before and 120 min after the procedure. Serum procalcitonin (PCT), serum ferritin, and urine B2MG analysis were done using enzyme-linked fluorescent assay (ELFA) and the magnetic Luminex® multiplex performance assay was used to analyse IL-6, IL-8, IL-10 and TNF-α plasma concentrations. Data on clinical outcomes were collected from patients’ medical records.

Results
Following TTPB, significant (p ≤ 0.05) increases were observed in uB2MG, IL-6, IL-8, IL-10 and TNF-α. Significant decreases were observed in ferritin (p ≤ 0.05). No significant change was observed in PCT concentration (p ≥ 0.05). One patient developed an infection and severe haematuria post-operatively following TTPB.

Conclusion
Although not confirmative, changes seen in biomarkers such as uB2MG, IL-10 and TNF-α in our observational clinical pilot-study may warrant further investigation, involving larger cohorts, to fully understand the role of these biomarkers and their potential association with post-operative complications such as infection and bleeding which can develop following TTPB for the diagnosis of PCa and BPH.
Traditional herbs against COVID-19: back to old weapons to combat the new pandemic
Authors: Al-kuraishy Hayder M. , Al-Fakhrany Omnia Momtaz , Elekhnawy Engy , Al-Gareeb Ali I. , Alorabi Mohammed , De Waard Michel , Albogami Sarah M. , Batiha Gaber El-Saber 
Published: September 2022

Abstract
Background
Recently, the coronavirus (COVID-19) pandemic is a chief public health disaster caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are no established effective preventive or therapeutic anti-COVID-19 drugs available except for some recently approved vaccines. Still, countless recent studies recommend various alternative and complementary approaches against COVID-19, which are medicinal herbs employed as traditional remedies to enhance immunity to struggle with viral infections. In addition, physicians worldwide are highly interested in vitamin and mineral supplements to help them combat COVID-19 either through protection or treatment. Dietary supplements specifically vitamin D, vitamin C, and zinc provide good prophylactic and therapeutic support to the presently available treatment regimens. In the present work, we have focused on plant-based remedies with promising anti-COVID-19 activities.

Aim
To enable investigators and researchers to identify potential herbal compounds with anti-COVID activity to be used as promising therapies to combat this pandemic.

Main body
This review highlights the recently published studies concerning natural traditional herbs, herbal bioactive metabolites, dietary supplements, and functional foods that could help prevent and/or treat COVID-19. Herein, we explored medicinal herbs as potential inhibitors of SARS-CoV-2 and discussed how these studies help form larger discussions of diet and disease. Moreover, by investigating the herbal bioactive components, we have outlined several medicinal herbs that can fight against COVID-19 by hindering SARS-CoV-2 replication and entry to its host cells, deterring the cytokine storm, and several other means. Finally, we have summarized various herbal products, functional foods, and dietary supplements with potent bioactive compounds which can inhibit and/or prevent COVID-19 disease progression.

Conclusions
Based on the studies reviewed in this work, it was concluded with no doubt that phytochemical components present in various herbs could have a starring role in the deterrence and cure of coronavirus contagion.
A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle
Authors: Teseo S. , Otani S. , Brinch C. , Leroy S. , Ruiz P. , Desvaux M. , Forano E. , Aarestrup F. M. , Sapountzis P. 
Published: September 2022

Abstract
Background
The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.

Results
Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.

Conclusions
Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task.
Transcriptomic and proteomic analyses provide insights into the adaptive responses to the combined impact of salinity and alkalinity in Gymnocypris przewalskii
Authors: Wei Fulei , Liang Jian , Tian Wengen , Yu Luxian , Feng Zhaohui , Hua Qiang 
Published: September 2022

AbstractGymnocypris przewalskiiis the only high-land endemic teleost living in Qinghai Lake, the largest saline–alkaline lake in China. Its osmoregulatory physiology remains elusive due to a lack of precise identification of the response proteins. In the present study, DIA/SWATH was used to identify differentially expressed proteins (DEPs) under alkaline (pH = 10.1, carbonate buffer), saline (12‰, sodium chloride), and saline–alkaline [carbonate buffer (pH = 10.1) plus 11‰ sodium chloride] stresses. A total of 66,056 unique peptides representing 7,150 proteins and 230 DEPs [the false discovery rate (FDR) ≤ 0.05, fold change (FC) ≥ 1.5] were identified under different stresses. Comparative analyses of the proteome and transcriptome indicated that over 86% of DEPs did not show consistent trends with mRNA. In addition to consistent enrichment results under different stresses, the specific DEPs involved in saline–alkaline adaptation were primarily enriched in functions of homeostasis, hormone synthesis and reactions of defense response, complement activation and reproductive development. Meanwhile, a protein–protein interaction (PPI) network analysis of these specific DEPs indicated that the hub genes were ITGAX, MMP9, C3, F2, CD74, BTK, ANXA1, NCKAP1L, and CASP8. This study accurately isolated the genes that respond to stress, and the results could be helpful for understanding the physiological regulation mechanisms regarding salinity, alkalinity, and salinity–alkalinity interactions.Graphical Abstract
Laparoscopic distal gastrectomy for advanced gastric cancer with situs inversus totalis: a case report
Authors: Fujita Shunsuke , Etoh Tsuyoshi , Kono Yohei , Fujishima Hajime , Suzuki Kosuke , Ninomiya Shigeo , Ueda Yoshitake , Shiroshita Hidefumi , Shiraishi Norio , Inomata Masafumi 
Published: September 2022

Abstract
Background
Situs inversus totalis (SIT) is a relatively rare condition, in which the thoracic and abdominal organs are reversed or mirrored from their normal positions. Here, we reported a case of a patient with SIT and advanced gastric cancer with lymph node metastasis who underwent laparoscopic distal gastrectomy (LDG).

Case presentation
A 67-year-old man with SIT was clinically diagnosed with T3N2M0 advanced gastric cancer located in the middle gastric body. Three-dimensional reconstruction of computed tomography angiogram revealed that the common hepatic artery originated from the superior mesenteric artery. The patient underwent LDG with D2 lymph node dissection and Roux-en-Y reconstruction. The postoperative course was uneventful.

Conclusion
This case report showed that LDG could be safely performed on a patient even under complex conditions, such as advanced gastric cancer with lymph node metastasis with SIT and vascular anomalies.
Successful laparoscopic repair for reduction en masse of infantile inguinal hernia: a case report of this rare condition
Authors: Yano Keisuke , Sugita Koshiro , Yamada Koji , Matsui Mayu , Yamada Waka , Kedoin Chihiro , Murakami Masakazu , Harumatsu Toshio , Onishi Shun , Kawano Takafumi , Muto Mitsuru , Ieiri Satoshi 
Published: September 2022

Abstract
Background
Reduction en masse (REM) is a rare condition following manual inguinal hernia (IH) reduction in which a hernia sac is reduced back into the preperitoneal space with a loop of the bowel incarcerated at the neck of the sac. It resembles successful manual reduction and may thus be overlooked easily. We herein report an infantile case of REM of an IH that was successfully treated laparoscopically.

Case presentation
A 10-month-old boy with a surgical history of bilateral open IH repair at 4 months old presented with a bulge in his left groin and vomiting. A left incarcerated recurrent IH was suspected, and manual reduction was performed. The hernia was apparently reduced successfully, but abdominal distention and vomiting persisted. He was admitted for further observation due to the symptoms. On day 2 after admission, abdominal X-ray showed extensive small bowel obstruction (SBO). Enhanced computed tomography (CT) revealed protrusion of the small bowel with a closed-loop in the left groin. A closed-loop SBO due to postoperative adhesion or an internal hernia was suspected. To assess the etiology of SBO, emergent laparoscopic exploration with hernia repair was planned. Laparoscopy revealed REM of the left incarcerated IH with a thickened peritoneum at the neck of the sac. Laparoscopic reduction was performed, and the incarcerated small bowel showed no signs of ischemia. The hernia sac was not associated with the previously ligated processes vaginalis, which had been closed by a previous Potts’ procedure. It was located at the inside of the processes vaginalis. The sac was successfully closed by laparoscopic percutaneous extraperitoneal closure procedures, and iliopubic tract repair was also performed via the previous inguinal incision. The postoperative course was uneventful.

Conclusion
Pediatric IH is due to the patent processes vaginalis, and REM is extremely rare. Laparoscopic surgery for REM is a relatively common and useful approach for the diagnosis and treatment of adults. In our infantile case, the laparoscopic approach was similarly effective for both investigating the cause of SBO and performing high ligation of the sac for this rare condition with IH.
Description of a telephone and Internet-based intervention to improve community responses to COVID-19 spread
Authors: Guruge Galmangoda Najith Duminda , Rathnayake Nadeeka , Abhayasinghe Kalpani 
Published: September 2022

Abstract
Background
This paper describes the process and results of a health promotion intervention to engage lay communities using telephone and online communication, to improve their current responses to the spread of COVID-19.

Methods
An intervention was conducted from March to July 2020 in three districts of Sri Lanka. Seven ‘trigger’ stories were shared through telephone or online communication to stimulate brainstorming and to engage selected community members. Determinants were identified and prioritised through discussions, and potentially beneficial actions were implemented as agreed by participants. The process was monitored, outcomes were evaluated monthly, and activities were modified according to ongoing observations.

Results
A total of 638 families (both adults and children) involved actively in implementing useful actions and reported an increased sense of personal control. Potential risk groups, best feasible community safety precautions and preparation to face challenges in the event of infection reaching their community were identified during brainstorming sessions with community mobilisers. A majority reported that they felt more confident, united and less anxious about handling potential risks and problems. Other beneficial outcomes include lifestyle changes leading to healthier behaviours and a sense of greater control over the conditions that govern their lives.

Conclusion
Use of telephone and online communication was effective in generating desirable community changes.
Identification of tubulointerstitial genes and ceRNA networks involved in diabetic nephropathy via integrated bioinformatics approaches
Authors: Cao Haiyan , Rao Xiaosheng , Jia Junya , Yan Tiekun , Li Dong 
Published: September 2022

Abstract
Background
Diabetic nephropathy (DN) is the major cause of end-stage renal disease worldwide. The mechanism of tubulointerstitial lesions in DN is not fully elucidated. This article aims to identify novel genes and clarify the molecular mechanisms for the progression of DN through integrated bioinformatics approaches.

Method
We downloaded microarray datasets from Gene Expression Omnibus (GEO) database and identified the differentially expressed genes (DEGs). Enrichment analyses, construction of Protein–protein interaction (PPI) network, and visualization of the co-expressed network between mRNAs and microRNAs (miRNAs) were performed. Additionally, we validated the expression of hub genes and analyzed the Receiver Operating Characteristic (ROC) curve in another GEO dataset. Clinical analysis and ceRNA networks were further analyzed.

Results
Totally 463 DEGs were identified, and enrichment analyses demonstrated that extracellular matrix structural constituents, regulation of immune effector process, positive regulation of cytokine production, phagosome, and complement and coagulation cascades were the major enriched pathways in DN. Three hub genes (CD53, CSF2RB, and LAPTM5) were obtained, and their expression levels were validated by GEO datasets. Pearson analysis showed that these genes were negatively correlated with the glomerular filtration rate (GFR). After literature searching, the ceRNA networks among circRNAs/IncRNAs, miRNAs, and mRNAs were constructed. The predicted RNA pathway of NEAT1/XIST-hsa-miR-155-5p/hsa-miR-486-5p-CSF2RB provides an important perspective and insights into the molecular mechanism of DN.

Conclusion
In conclusion, we identified three genes, namely CD53, CSF2RB, and LAPTM5, as hub genes of tubulointerstitial lesions in DN. They may be closely related to the pathogenesis of DN and the predicted RNA regulatory pathway of NEAT1/XIST-hsa-miR-155-5p/hsa-miR-486-5p-CSF2RB presents a biomarker axis to the occurrence and development of DN.
A re-assessment of Taxomyces andreanae, the alleged taxol-producing fungus, using comparative genomics
Authors: Cheng Tian , Kolařík Miroslav , Quijada Luis , Stadler Marc 
Published: September 2022

AbstractThe monotypic “bulbilliferous hyphomycete” genus Taxomyces was erected in 1993 for a fungal endophyte isolated from the Yew tree Taxus brevifolia and named Taxomyces andreanae. This fungus was reported to produce the plant-derived anti-cancer drug taxol. The original description of the fungus was not conclusive as to its taxonomic position because no sporulation or other salient morphological features were reported. Consequently, the taxonomic affinities of this fungus have remained obscure. However, a full genome sequence of this strain was generated by a German research group in 2013, in an unsuccessful attempt to detect the biosynthesis genes encoding for taxol. This prompted us to search for phylogenetic marker genes and compare those with the data that recently have become available from state-of-the-art polyphasic taxonomic studies. Surprisingly, the strain turned out to belong to the phlebioid clade of wood-destroying Basidiomycota as inferred from a comparison of its partial ITS, the 28S rDNA (LSU), the RNA polymerase II largest subunit (rpb1), the RNA polymerase II second largest subunit (rpb2), and the translation elongation factor 1-α (tef1) sequences. A multi gene genealogy based on these loci revealed that the closest relative is Ceriporiopsis (syn. Mycoacia) gilvescens. Even though such wood-destroying Basidiomycota are regularly encountered among the endophytic isolates after surface-disinfection of plant organs, the vast majority of the reported endophytic fungi belong to the Ascomycota. Nevertheless, the data available now allow for synonymizing Taxomyces with Ceriporiopsis, and the necessary new combination is made.
How to Feed an Empire?
Authors: Sollai Michele 
Published: September 2022

AbstractIn 1937—one year after the Fascist “conquest” of Ethiopia—the Italian East African Empire was on the brink of an economic and food crisis. In order to feed the newborn empire's growing Italian population, Mussolini's regime launched a call for agricultural mobilization meant to rapidly make the empire self-sufficient in wheat, the main staple of the Italian population. This article analyzes the scientific foundations of the program of imperial “wheat autarky” and its materialization during the “wheat campaigns” between 1938 and 1941, particularly focusing on the introduction of and experimentation with hybrid wheat seeds in the Ethiopian highlands. The article shows the key role played by Italian agronomists and plant breeders in the framing and implementation of wheat autarky in the Fascist empire. Contrary to the historical emphasis of Fascist propaganda on the technological and human colonization of Ethiopia by Italian agriculture, the article also argues for the crucial position of indigenous farming within the colonial project of wheat development. Finally, Ethiopia's environments and its nonhuman actors became essential protagonists in the unfolding of these agricultural plans. The article makes the case for viewing wheat rust—a fungal plant disease—as a key component of the evolution and demise of the Italian occupation of Ethiopia.
A microfluidic platform to investigate the role of mechanical constraints on tissue reorganization
Authors: Tlili Sham L. , Graner François , Delanoë-Ayari Hélène 
Published: September 2022

ABSTRACT
Mechanical constraints have a high impact on development processes, and there is a need for new tools to investigate the role of mechanosensitive pathways in tissue reorganization during development. We present here experiments in which embryonic cell aggregates are aspired through constrictions in microfluidic channels, generating highly heterogeneous flows and large cell deformations that can be imaged using two-photon microscopy. This approach provides a way to measure in situ local viscoelastic properties of 3D tissues and connect them to intracellular and intercellular events, such as cell shape changes and cell rearrangements. These methods could be applied to organoids to investigate and quantify rheological properties of tissues, and to understand how constraints affect development.
The complete mitochondrial genome sequence of Chimarrogale leander (Insectivora: Soricidae)
Authors: Miao Yongxin , Li Yidi , Mei Yaqing , Chen Cheng , Sun Liling , Zhang Baowei , Wang Hui 
Published: September 2022

Background: Chimarrogale leander is a species of the family Soricidae and is mainly distributed in southern China. Methods: Here, a complete mitochondrial genome for C. leander was assembled via high-throughput sequencing technology. Results The results showed that the complete mitogenome of C. leander is 17,357 bp and includes 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%. Through the phylogenetic analysis of complete mitochondrial genome, it is found that C. leander has a close genetic relationship with Nectogale elegans. Conclusions: The new mitogenome will hopefully prove useful for systematic analyses of genus Chimarrogale.