bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drosophila FMRP controls miR-276-mediated regulation of nejire mRNA for space-filling dendrite development
Authors: Li Hui , Gavis Elizabeth R 
Published: September 2022

Abstract
MicroRNAs are enriched in neurons and play important roles in dendritic spine development and synaptic plasticity. MicroRNA activity is controlled by a wide range of RNA-binding proteins. FMRP, a highly conserved RNA-binding protein, has been linked to microRNA-mediated gene regulation in axonal development and dendritic spine formation. FMRP also participates in dendritic arbor morphogenesis, but whether and how microRNAs contribute to its function in this process remains to be elucidated. Here, using Drosophila larval sensory neurons, we show that a FMRP-associated microRNA, miR-276, functions in FMRP-mediated space-filling dendrite morphogenesis. Using EGFP microRNA sensors, we demonstrate that FMRP likely acts by regulating miR-276a RNA targeting rather than by modulating microRNA levels. Supporting this conclusion, miR-276a coimmunoprecipitated with FMRP and this association was dependent on the FMRP KH domains. By testing putative targets of the FMRP–miR-276a regulatory axis, we identified nejire as a FMRP-associated mRNA and, using EGFP reporters, showed that the nejire 3′ untranslated region is a target of miR-276a in vivo. Genetic analysis places nejire downstream of the FMRP–miR-276a pathway in regulating dendrite patterning. Together, our findings support a model in which FMRP facilitates miR-276a-mediated control of nejire for proper dendrite space-filling morphology and shed light on microRNA-dependent dendrite developmental pathology of fragile X syndrome.
Higher Cell-Mediated Immune Responses in Patients With Inflammatory Bowel Disease on Anti-TNF Therapy After COVID-19 Vaccination
Authors: Caldera Freddy , Farraye Francis A , Necela Brian M , Cogen Davitte , Saha Sumona , Wald Arnold , Daoud Nader D , Chun Kelly , Grimes Ian , Lutz Megan , Van Helden Sean R , Swift Melanie D , Virk Abinash , Bharucha Adil E , Patel Tushar C , Gores Gregory J , Chumsri Saranya , Hayney Mary S , Knutson Keith L 
Published: September 2022

Abstract

Background
Some patients with inflammatory bowel disease (IBD) on immunosuppressive therapies may have a blunted response to certain vaccines, including the messenger RNA (mRNA) coronavirus disease 2019 (COVID-19) vaccines. However, few studies have evaluated the cell-mediated immune response (CMIR), which is critical to host defense after COVID-19 infection. The aim of this study was to evaluate the humoral immune response and CMIR after mRNA COVID-19 vaccination in patients with IBD.

Methods
This prospective study (HERCULES [HumoRal and CellULar initial and Sustained immunogenicity in patients with IBD] study) evaluated humoral immune response and CMIR after completion of 2 doses of mRNA COVID-19 vaccines in 158 IBD patients and 20 healthy control (HC) subjects. The primary outcome was the CMIR to mRNA COVID-19 vaccines in patients with IBD. The secondary outcomes were a comparison of (1) the CMIR in patients with IBD and HC subjects, (2) CMIR and humoral immune response in all participants, and (3) correlation between CMIR and humoral immune response.

Results
The majority (89%) of patients with IBD developed a CMIR, which was not different vs HC subjects (94%) (P = .6667). There was no significant difference (P = .5488) in CMIR between immunocompetent (median 255 [interquartile range, 146-958] spike T cells per million peripheral blood mononuclear cells) and immunosuppressed patients (median 377 [interquartile range, 123-1440]). There was no correlation between humoral and cell-mediated immunity after vaccination (P = .5215). In univariable analysis, anti-tumor necrosis factor therapy was associated with a higher CMIRs (P = .02) and confirmed in a multivariable model (P = .02). No other variables were associated with CMIR.

Conclusions
Most patients with IBD achieved CMIR to a COVID-19 vaccine. Future studies are needed evaluating sustained CMIR and clinical outcomes.
Co-designing marine science beyond good intentions: support stakeholders’ empowerment in transformative pathways
Authors: Cazé Cosma , Mazé Camille , Danto Anatole , Saeedi Hanieh , Lear Dan , Suominen Saara , Ginigini Joape , Brodie Gilianne , Korovulavula Isoa , Pinto Isabel Sousa 
Published: September 2022

AbstractCalls for science to innovate by including stakeholders' in the creation of marine knowledge have been rising, to create impact beyond laboratories and to contribute to the empowerment of local communities when interacting with marine and coastal ecosystems. As a transdisciplinary group of scientists working on co-designing research projects, this paper draws upon our experiences to further define the concept and seek to improve the process of co-design. We highlight the key barriers for co-design processes to contribute to increasing stakeholders' capacity to produce intended effects on marine policy. We suggest that stakeholder engagement requires overcoming the resistance to non-scientific knowledge sources and considering power asymmetries in the governance and management of the ocean. We argue that power and politics must be placed at the very heart of the production of a co-designed marine science and must be an aspect of the facilitation itself. In this paper, we aim to provide insights to navigate throughout the journey of stakeholder engagement, with the critical perspective necessary to make this process socially and environmentally effective.
Ocean acidification research for sustainability: co-designing global action on local scales
Authors: Dobson K L , Newton J A , Widdicombe S , Schoo K L , Acquafredda M P , Kitch G , Bantelman A , Lowder K , Valauri-Orton A , Soapi K , Azetsu-Scott K , Isensee K 
Published: September 2022

AbstractThe global threat that ocean acidification poses to marine ecosystems has been recognized by the UN 2030 Agenda under Sustainable Development Goal, Target 14.3: to reduce ocean acidification. The Global Ocean Acidification Observing Network (GOA-ON) is a collaborative international network to detect and understand the drivers of ocean acidification in estuarine-coastal-open ocean environments, the resulting impacts on marine ecosystems, and to make the information available to optimize modelling studies. The Ocean Acidification Research for Sustainability (OARS) programme, endorsed by the 2021–2030 UN Decade of Ocean Science for Sustainable Development, will build on the work of GOA-ON through its seven Decade Action Outcomes. By employing a Theory of Change framework, and with the co-design of science in mind, OARS will develop an implementation plan for each Decade Action Outcome, which will identify the stakeholders and rights-holders, as well as the tools, means, and positive consequences required for their successful delivery. The organizational structure of GOA-ON, with nine regional hubs, will benefit OARS by providing a vital connection between local and global scales. GOA-ON regional hub case-studies illustrate how activities in the past and future, informed by global and regional priorities, support capacity building and the co-design of ocean acidification science.
Efficacy and safety of intraoperative cone-beam CT-guided localization of small pulmonary nodules
Authors: Kaiho Taisuke , Suzuki Hidemi , Hata Atsushi , Ito Takamasa , Tanaka Kazuhisa , Sakairi Yuichi , Kato Hideyuki , Shiko Yuki , Kawasaki Yohei , Yoshino Ichiro 
Published: September 2022

Abstract

OBJECTIVES
This study aimed to evaluate the efficacy and safety of intraoperative cone-beam computed tomography-guided video-assisted thoracoscopic surgery wedge resection of impalpable small pulmonary nodules.

METHODS
This was a single-centre phase 2 trial conducted between April 2018 and March 2019. Peripheral small pulmonary nodules, defined as either ground-glass opacity-dominant (&gt;50%) nodules measuring ≤3 cm in diameter (ground-glass opacity-dominant type) or nodules measuring ≤2 cm in diameter located deeper than the nodule diameter from the visceral pleura (deep solid type), were eligible for resection using a cone-beam computed tomography-guided thoracoscopic manner. The primary end-point was macroscopic complete resection, and secondary end-points were: nodule extraction rate, operation time, localization time, marking accuracy, microscopic complete resection and safety.

RESULTS
Twenty-two nodules, in 9 men and 11 women with a mean age of 64.3 years, were visualized and resected. The nodules were located in the right upper, middle and lower lobes in 3, 1 and 5 patients, respectively, and in the left upper and lower lobes in 5 and 8 patients, respectively. Seven nodules were ground-glass opacity-dominant types, and 15 were deep solid types. Cone-beam computed tomography could clearly image all nodules. The mean time for localization was 17.4 min. The mean operation time was 110.7 min. Macroscopic complete resection was accomplished in 21 nodules (95.5%). Microscopic complete resection was achieved in all nodules (100%). Postoperative air leakage and bleeding were observed in 1 patient (5%).

CONCLUSIONS
Cone-beam computed tomography might be a safe and useful guide for video-assisted thoracoscopic surgery wedge resection of impalpable peripheral pulmonary nodules.

Date and number of IRB approval
15 November 2017, 381.

Clinical trial registration number
UMIN 000030388.
Analysis of Six Human Milk Oligosaccharides (HMO) in Infant Formula and Adult Nutritionals by 2AB Labeling and Quantification with HILIC-FLD: First Action 2022.02
Authors: Ellingson David J , Ruosch Andrew J , Foster Kalley L , Duchniak Kaitlyn M , Laessig Ian M 
Published: September 2022

Abstract

Background
Human milk oligosaccharides (HMO) function as a prebiotic, enhance immune functions, and support brain development for infants when fed mother’s milk. These are added to infant formula and adult nutritionals in order provide these same benefits.

Objective
To develop and validate a method that can meet the AOAC Standard Method Performance Requirements (SMPR®) outlined by the AOAC INTERNATIONAL Stakeholder Panel for Infant Formula and Adult Nutritionals (SPIFAN) through a single-laboratory validation (SLV).

Methods
This work describes a method that can analyze six different HMOs that include 2’-fucosyllactose, 3-fucosyllactose, 3’-sialyllactose, 6’-sialyllactose, lacto-N-tetraose, and lacto-N-neotetraose. The method utilizes a derivatization procedure that labels the HMO with the fluorescent compound 2-aminobenzamide. The method was optimized to provide a non-toxic derivatization procedure, automate the removal of excess derivatization reagent, and provide a chromatographic separation that can analyze multiple HMOs in a single profile.

Results
A summary from the SLV is provided.

Conclusion
The SLV was reviewed by the AOAC SPIFAN Expert Review Panel, and determined the method met the SMPR requirements for six HMO.

Highlights
The method was granted First Action Official MethodsSM status.
Effects of high- and low-fiber diets on intestinal oxidative stress in growing-finishing pigs
Authors: Jin Shunshun , Wijerathne Charith U B , Au-Yeung Kathy K W , Lei Huaigang , Yang Chengbo , O Karmin 
Published: September 2022

Abstract
Feed is the most expensive facet of commercial pork production. In order to reduce feed costs, using high-fiber ingredients has become a common practice. Moderate levels of fiber can maintain intestinal physiological function and promote intestinal health. Oxidative stress is linked to impaired nutrient absorption and growth performance. This study investigated the effects of high-fiber (5.26% crude fiber) and low-fiber (2.46% crude fiber) diets on growth performance and intestinal oxidative stress parameters in growing-finishing pigs. Forty growing pigs with initial body weight (27.07 ± 1.26 kg) were randomly assigned to 2 treatment groups with 10 replicates of 2 pigs per pen. Pigs were weighed on day 35, 42, and 70. The feed intake was recorded daily to calculate growth performance parameters. On day 70, eight pigs in each treatment group were randomly selected and euthanized to obtain jejunum to measure oxidative stress status. Pigs fed a high-fiber diet were heavier than those fed a low-fiber diet on days 35, 42, and 70 (P &lt; 0.05). During the whole feeding period, pigs fed a high-fiber diet had a higher average daily gain than those fed a low-fiber diet (P &lt; 0.05). The low-fiber diet resulted in increased levels of malondialdehyde (P &lt; 0.05) in the jejunum, suggesting that the low-fiber diet contributed to oxidative stress in the jejunum. The low-fiber diet also led to a significant increase in glutathione and oxidized glutathione levels (P &lt; 0.05) in the jejunum, indicating that pigs fed a low-fiber diet needed to produce more antioxidant substances to cope with oxidative stress in the intestine. This was accompanied by a significant increase in the expression of glutathione synthesizing enzymes in the jejunum of the low-fiber group (P &lt; 0.05). These results suggest that the high-fiber diet can improve growth performance and maintain intestinal health in growing-finishing pigs by reducing intestinal oxidative stress.
Adenoid Cystic Carcinoma of the Breast: Radiologic-Pathologic Correlation
Authors: Vijapura Charmi , Rosen Lauren , Wahab Rifat 
Published: September 2022

Abstract
Adenoid cystic carcinoma (ACC) is an uncommon malignancy occurring most frequently in the salivary glands. Breast ACC is rare. Pain is common at the site of ACC; otherwise, presentation is similar to other primary breast cancers. Adenoid cystic carcinomas classically lack calcifications; the imaging manifestations of ACC are otherwise highly variable, likely related to multiple pathologic growth patterns. While ACC in other regions of the body tends to be more aggressive, ACC involving the breast typically has less aggressive biologic characteristics. Classic-type breast ACC has a lower tendency to recur locally with radiation, metastasize to regional lymph nodes, and spread to other parts of the body. Perineural spread of disease can be seen but is not common. The rarer solid basaloid–type has a higher tendency for local or distant spread and recurrence. Although ACC is usually triple receptor–negative (estrogen receptor, progesterone receptor, human epidermal growth factor-2 receptor), the indolent nature of this tumor dictates its management. With classic-type ACC, the inclusion of axillary surgery has no consensus and the use of chemotherapy or hormonal therapy is rare. Axillary nodal surgery and chemotherapy are often included in management of the more aggressive solid basaloid–type. An understanding of the breast imaging, histopathology, and clinical course is key for appropriate treatment and follow-up of ACC.
White rhinos and other herbivores decrease visitations and increase vigilance in response to human vocalizations
Authors: Nhleko Zoliswa N , Shrader Adrian M , Ferreira Sam M , McCleery Robert A 
Published: September 2022

Abstract
Harnessing the fear animals have of humans has the potential to aid in the conservation of wildlife. Most vertebrates perceive humans as “super predators.” While predator cues are an important nonlethal management tool, the use of human cues for management has rarely been implemented or experimentally tested. Extensive poaching is threatening the persistence of white rhinos (Ceratotherium simum simum), and there is a need to deter them from areas with elevated poaching risks. To investigate the feasibility of harnessing the fear white rhinos have of humans to aid in their conservation, we conducted playback experiments at rhino middens. We broadcasted repeated human (treatment) and bird (control) vocalizations, and measured changes in visitations and antipredator responses. We found that overall rhino visitations did not change in response to controls but decreased by 46% in response to human vocalizations. This pattern appears to be driven by the response of females, who decreased their visitations by 70% in response to human vocalizations, while visitations by males remained unchanged. This difference is likely related to males defending small exclusive territories. Providing evidence that changes in female visitation rates were a function of the perceived fear of white rhinos, we found that both sexes exhibited more vigilance in response to human vocalizations (males 69.5%, females 96%) compared to controls. We also saw a 63% reduction of other herbivores at treatment sites. Our findings provide evidence that the fear of humans can be used to alter the movements and behavior of female white rhinos, critical for population recovery, as well as other large herbivores.
Acari (Parasitiformes and Acariformes) From Mexico: Analysis of Their Geographical and Host Distribution in Rodentia (Cricetidae)
Authors: Herrera-Mares Angel , Guzmán-Cornejo Carmen , García-Prieto Luis , Rebollo-Hernández Andrea , León-Paniagua Livia , Del Castillo-Martínez Laura , Montiel-Parra Griselda , Ríos-Sais Gerardo 
Published: September 2022

Abstract
The study of Acari associated with cricetid rodents in Mexico began at the end of the 1930s. Despite efforts to gathering the information, only listings were built, but none of these studies present an analysis of the available data. A search was made through electronic databases; in addition, some not published records contained at Collection of Laboratorio de Acarología, Facultad de Ciencias, Universidad Nacional Autónoma de México were included in the inventory. Combining the literature records and those deposited in the collection, the total number of species of Acari associated with this family of rodents is 165, distributed in two superorders, four orders, 15 families, and 57 genera. Of the 15 families registered, the richest is Trombiculidae (70 nominal species and 75 taxa), followed by Laelapidae (39 and 42, respectively), Ixodidae (13 nominal and 16 taxa), and Leewenhoekiidae (13 nominal and taxa). From the bibliographic searches, a total of 76 papers were recovered with information on the association between Acari and cricetid rodents in Mexico. The main detected approach in the literature was taxonomic (75 works) and one on detection of pathogens. From the 145 known species of cricetids recorded in Mexico, only 72 (distributed in 18 genera) have been studied and found to host Acari. The use of regionalization of Mexico in provinces allowed us to map the records of Acari associated to cricetids in the most natural approximation of their distribution. We recognize and discuss seven factors that favor the scarcity and asymmetry of acarological studies in Mexico.
Resistance of Basal Forebrain Cholinergic Neurons to TDP-43 Proteinopathy in Primary Progressive Aphasia
Authors: Dunlop Sara Rose , Ayala Ivan , Spencer Callen , Flanagan Margaret E , Mesulam Marek-Marsel , Gefen Tamar , Geula Changiz 
Published: September 2022

Abstract
Basal forebrain cholinergic neurons (BFCN) display accumulation of neurofibrillary tangles and degeneration in Alzheimer disease and are targets of therapeutic intervention. This study determined vulnerability of BFCN to accumulation of TDP-43 in primary progressive aphasia with TDP-43 proteinopathy (PPA-TDP). Brains from 16 PPA participants with pathologically confirmed TDP-43 proteinopathy, with available paraffin-embedded sections (Group 1), or systematically sampled frozen sections (Group 2), were studied. Immunohistochemistry was performed with an antibody against phosphorylated TDP-43. BFCN were identified by their magnocellular appearance in Nissl preparations. Presence of TDP-43 inclusions and preinclusions in BFCN was determined and quantitative analysis was performed in Group 2. In Group 1, BFCN were completely free of inclusions except for occasional dystrophic neurites. Sparse TDP-43 preinclusions with smooth or granular staining in BFCN were detected. In Group 2, extremely rare TDP-43 intranuclear inclusions were detected in 0.1% of BFCN per section, along with occasional dystrophic neurites. Although sparse, significantly more preinclusions (1.4% of BFCN) were present when compared with inclusions. No hemispheric differences were noted. Small neurons near BFCN contained more preinclusions compared with BFCN. Thus, BFCN in PPA-TDP are resistant to TDP-43 proteinopathy and degeneration, suggesting that cholinergic therapy is unlikely to be effective in this disorder.
Sentiment analysis in cross-linguistic context: How can machine translation influence sentiment classification?
Authors: Bilianos Dimitris , Mikros George 
Published: September 2022

AbstractIn recent years, there has been a lot of interest in cross-language sentiment classification, as the research in sentiment analysis has shifted focus from English to less resourceful languages. Cross-language sentiment classification attempts to leverage the automated machine translation (MT) capability utilizing the infrastructure of languages rich in linguistic resources, mainly English, to help build sentiment analysis systems for low-resource languages. In this study, we explore how MT influences cross-language sentiment classification. To this end, we perform three different experiments, obtaining promising results. In the first experiment, we automatically translate 4,000 positive and negative reviews from English into Greek and Italian, thus obtaining labeled sentiment datasets in these languages. Then, we train a Naive Bayes classifier and compare the performance with the source dataset. In the second experiment, the translated reviews are automatically translated back into the source language (English), aiming to compare the classification accuracy with the one obtained in the original dataset. In the final approach, the reviews are translated from the source (English) into Italian through an intermediate translation in Greek to examine whether the performance was further diminished compared with the approach of the first experiment.
Mitochondrial Genomes inPerkinsusDecode Conserved Frameshifts in All Genes
Authors: Gornik Sebastian G , Flores Victor , Reinhardt Franziska , Erber Lieselotte , Salas-Leiva Dayana E , Douvropoulou Olga , Lassadi Imen , Einarsson Elin , Mörl Mario , Git Anna , Stadler Peter F , Pain Arnab , Waller Ross F 
Published: September 2022

AbstractMitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.