bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathway Centric Analysis for single-cell RNA-seq and Spatial Transcriptomics Data with GSDensity
Authors: Liang Qingnan , Chen Ken 
Published: November 2022

Abstract
Advances in single-cell technology have enabled molecular cellular dissection of heterogeneous biospecimens at unprecedented scales and resolutions. Although cluster-centric approaches followed by gene-set analysis can reveal distinct cell types and states, they have limited power in dissecting and interpretating highly heterogenous, dynamically evolving data. Here, we present GSDensity, a graph-modeling approach that allows users to obtain pathway-centric interpretation and dissection of single-cell and spatial transcriptomics (ST) data without performing clustering. We show that GSDensity can not only accurately detect biologically distinct gene sets but also reveal novel cell-pathway associations that are ignored by existing methods. This is particularly evident in characterizing cancer cell states that are transcriptomically distinct but are driven by shared tumor-immune interaction mechanisms. Moreover, we show that GSDensity, combined with trajectory analysis can identify pathways that are active at various stages of mouse brain development. Finally, we show that GSDensity can identify spatially relevant pathways in mouse brains including those following a high-order organizational patterns in the ST data. We also created a pan-cancer pathway activity ST map, which revealed pathways spatially relevant and recurrently active across six different tumor types. GSDensity is available as an open-source R package and can be widely applied to single-cell and ST data generated by various technologies.
Effects of dopamine-based genetic risk score on dynamic low-frequency fluctuations in patients with first-episode drug-naïve schizophrenia
Authors: Kang Yafei , Zhang Youming , Huang Kexin , Wang Zhenhong 
Published: November 2022

Abstract
Alterations in dynamic intrinsic brain activity and neurotransmitter signaling, such as dopamine, have been independently detected in schizophrenia patients. Yet, it remains unclear whether the dopamine genetic risk variants have additive effects on brain intrinsic activity. We aimed to investigate the schizophrenia-specific dynamic amplitude of low frequency fluctuation (dALFF) altered pattern, and its association with dopamine genetic risk score in first-episode drug-naïve schizophrenia (FES). Fifty-five FES and 53 healthy controls were included. A sliding-window method based on the dALFF was adopted to estimate the dynamic alterations in intrinsic brain activity. Subjects were genotyped, and a genetic risk score (GRS), which combined the additive effects of ten risk genotypes from five dopamine-related genes, was calculated. We used the voxel-wised correlation analysis to assess the effects of dopamine- GRS on dALFF. FES showed significantly increased dALFF left medial prefrontal cortex and significantly decreased dALFF in the right posterior cingulate cortex compared with healthy controls. Greater dopamine GRS in FES was associated with higher dALFF in the left middle frontal gyrus and left inferior parietal gyrus. Our findings indicate that cumulative dopamine genetic risk is associated with a known imaging phenotype for schizophrenia.
ATF6β deficiency elicits anxiety-like behavior and hyperactivity under stress conditions
Authors: Tanaka Takashi , Nguyen Dinh Thi , Kwankaew Nichakarn , Sumizono Megumi , Shinoda Reika , Ishii Hiroshi , Takarada-Iemata Mika , Hattori Tsuyoshi , Oyadomari Seiichi , Kato Nobuo , Mori Kazutoshi , Hori Osamu 
Published: November 2022

Abstract
Activating transcription factor 6 (ATF6) is an endoplasmic reticulum (ER) stress-regulated transcription factor that induces expression of major molecular chaperones in the ER. We recently reported that ATF6β, a subtype of the ATF6, induced expression of calreticulin, a molecular chaperone in the ER with a high Ca2+-binding capacity, and promoted neuronal survival against ER stress and excitotoxicity. In the present study, we demonstrate that ATF6β deficiency in mice also decreases calreticulin expression and increases expression of glucose-regulated protein 78, another ER molecular chaperone, in the emotional brain regions such as the prefrontal cortex (PFC), hypothalamus, hippocampus and amygdala. Comprehensive behavioral analyses revealed that Atf6b-/- mice exhibited anxiety-like behavior in the light/dark transition test and hyperactivity in the forced swim test. Consistently, PFC and hypothalamic corticotropin-releasing hormone (CRH) expression was increased in Atf6b-/- mice, as was circulating corticosterone. Moreover, CRH receptor 1 antagonism alleviated anxiety-like behavior in Atf6b-/- mice. These findings suggest ATF6β deficiency elicits anxiety-like behavior and hyperactivity in CRH receptor 1-dependent mechanism. ATF6β could play a role in psychiatric conditions in the emotional centers of the brain.
Scale-up Production and Immunological Assessment of Recombinant SARS- CoV-2 Spike RBD in Pichia pastoris
Authors: Raoufi Ehsan , Hosseini Fatemeh , Onagh Bahman , Salehi-Shadkami Mohammad , Mehrali Marjan , Mohsenzadegan Monireh , Farajollahi Mohammad M 
Published: November 2022

Abstract
With more than two years in COVID-19 pandemic, the underlying virus is mutating which indicates it is not over yet hence SARS-CoV-2 Spike RBD is a potent candidate for immunological development purposes. Here, we produced a recombinant-RBD protein from micro- to macro-scale production by Pichia pastoris with high purity that was assessed by immunological tests. A recombinant-RBD compromising 283 residues (31kDa) was constructed after epitope analyses. The target gene was initially cloned into Escherichia coli Top10 genotype and transformed into Pichia pastoris CBS7435 muts for protein production. The production was scaled-up in a 10L fermenter after 1L shake-flask cultivation. The product was ultrafiltered and purified using ION-Exchange chromatography. IgG-positive human sera for SARS-CoV-2 were employed by ELISA test to evaluate the antigenicity and specific binding of the produced protein. Bioreactor cultivation yielded 4g/L of target protein after 160 hours fermentation, and ion-exchange chromatography indicated a purity of > 95%. Human serum ELISA test performed in four parts (1–4) and ROC curve area under curve (AUC) was > 0.96 for each part. The mean specificity and sensitivity of each part was (100, 91.5) respectively. In conclusion, the recombinant-RBD can be used for IgG-based serologic kit and preventive purposes for patients with COVID-19 infection.
Convergence in Gender Inequality and Gender Development: A Panel Data Evidence
Authors: Trofimov Ivan D. 
Published: November 2022

Abstract
The paper examined convergence process and outcomes in gender indicators (gender inequality and development indexes) for two global panels of 106 and 75 economies over the 1990-2013 period. The five convergence dimensions were considered: beta, sigma, gamma, stochastic, and club convergence. The statistical methods included cross-sectional regression, kernel density plots, panel unit root tests, the rank correlation, and Phillips-Sul club convergence algorithm. While there reduction in gender inequality and improvement in gender development across the panel, the convergence in most dimensions was observed only for the gender development. Formation of the clubs and the absence of convergence to a single level were common for gender inequality. Overall, the findings indicate that improvement in gender development indicators did not translate into higher gender equality, thereby suggesting corrective policy action at national and international levels.
A primary small cell neuroendocrine carcinoma (SCNC) of the oral cavity (cheek mucosa): description of a case report
Authors: Longo Raffaele , Colin Sebastien , Streiff Camille , Benichou Claire Gamelon , Wendel Chloé , Campitiello Marco , Plastino Francesca , Bastien Claire , Egea Julie 
Published: November 2022

Abstract
Background
Small cell neuroendocrine carcinoma (SCNC) of the oral cavity is a poorly differentiated, high‐grade and very aggressive tumor with a poor prognosis.
Case Description
A 64-year-old, Caucasian, smoker man consulted for an ulcero-necrotic, exophytic, lesion of the right retromolar trigone. Haed&neck CT scan showed a right tonsillar tumor lesion. The 18F-PET scan confirmed the presence of a right, highly hypermetabolic tonsillar lesion and two homolateral, cervical lymph nodes. Histology and immunohistochemistry were consisted with the diagnosis of a primary SCNC of the oral cavity. As the tumor was locally advanced and unresectable, the patient underwent a definitive radio-chemotherapy with a cisplatin/etoposide combined regimen (4 cycles). The treatment was well tolerated and led to a complete tumor response.
Conclusion
The particularity of this case relies on the rarity of the oral SCNC, its difficult and challenging diagnosis, and the complexity of its management that is not validated by large clinical trials, data being extrapolated from small cell lung cancer. In our case, the patient presenting a locally advanced tumor was treated by a combined radio-chemiotherapy leading to a complete tumor regression. The patient’s follow up is too short to assess the real benefit of this treatment on overall survival.
Detail design (DD), front end (FE), back end (BD) design of non-tactical deployable 20 GWh (17.20841 kilo ton TNT) plane wave lens configuration fusion device
Authors: Rafique Muhammad Musaddique Ali 
Published: November 2022

Abstract
A simple plane wave lens, using an inert central plastic wave shaper, has been designed. An experiment was done with a 4 in diam, zeroth order design. An iterative technique that uses measured time deviations to connect the next wave shape was developed. Two identical versions of the first iterated shape were fired. Arrival time deviations in these first iterates fell within 50 ns bonds. With greater care and further iterations, lenses bound by 10 ns deviations seem possible. An advanced and novel integration method is applied. It is shown that this technique bears significant advantage over prior methods and is meritorious.
Church Forests Diversity and Biomass Carbon Stock Along Urbanization Continuum in Dangila District, Awi-Zone, Ethiopia
Authors: Sewagegn Geremew Bitew , Abate Dagm Fikir 
Published: November 2022

Abstract

Ethiopian Orthodox Tewahido Churches plays a significant role for native species conservation, carbon sequestration and climate change mitigation. The study was conducted to determine woody species diversity and biomass carbon stock of church forests along urbanization continuum in Dangila Woreda, Awi-zone, Ethiopia. After a preliminary survey, the churches were grouped into urban, peri-urban and rural continuums. Then one church was purposively selected from each urbanization continuum based on age gradient for making up a total of nine sample churches. Tree height and DBH data was recorded from a 2m width systematically laid down Gentry transect lines; whereas, seedlings was counted from three plots of 2m×2m size at each transect line. The similarities along urbanization were computed using Sorenson’s similarity index. Further ANOVA were used to test differences among the continuum. Finally, a total of 91 woody species were identified in the church forest. The mean Shannon diversity in urban, peri-urban and rural church forests was 2.38, 2.67 and 2.90 respectively. The general pattern of woody species community structure along urbanization continuum shows an inverted J-shape. The biomass carbon stock along urban, peri-urban and rural continuum was 24.96, 77.38and 46.13 metric tons respectively. Therefore, church forests are playing an indispensable role for woody species conservation, carbon sequestration and climate change mitigation at each urbanization continuum.
Biochar and legumes improve pastures in Brazil: environmental and socioeconomic analysis of three forage grasses in a field experiment
Authors: Latawiec Agnieszka E. , Rodrigues Aline F. , Korys Katarzyna Anna , Mendes Maiara S. , Rangel Marcio , Castro Ana , Teixeira Wenceslau , Valentim Judson F. , Araujo Ednaldo , de Moraes Luiz Fernando Duarte , Pacheco Vinicius , Mendes Marcos , Picolla Cristiano della , Strassburg Bernardo , Kubon Maciej , Drosik Adam , Gomes Fernanda , Reid Brian , Krieger Joana , Dib Viviane , Zarzly Dariusz 
Published: November 2022

Abstract

Pasturelands, often degraded, represent most of the converted lands globally. Here we present the results from a field experiment in Brazil where we tested the impact of different soil enhancers on soil quality and productivity of three tropical forages grasses: Brachiaria (Syn. Urochloa) brizantha cv. Marandu, Brachiaria brizantha cv. BRS Piatã, and Brachiaria brizantha cv. BRS Paiaguás. Soil enhancers included: biochar - a carbon-rich product from biomass pyrolysis, moinha, a local charcoal residue, traditional fertiliser containing nitrogen, phosphorus and potassium, lime and forage peanut (Arachis pintoi cv. Amarillo). Independent of treatment and Brachiaria cultivar, dry matter tended to be greatest in the first harvesting period, decreasing sharply in the second. Considering the total biomass produced over the experiment (sum of four harvests), the highest production (dry biomass) was for Piatã cultivar (14.07 Mg ha-1; treatment with the biochar application rate of 30 Mg ha-1). For Marandu and Piatã, the highest forage biomass increases were observed with the treatment that included biochar at the rate of 30 Mg ha-1. Marandu and Piatã yields generated an income of U$ 1,291 per year and U$ 1,183, respectively. For Paiaguas, the treatment that generated the greatest yield increase was forage peanut forage + 15 Mg ha-1 with its total income peak at U$ 991. The results reflected positive changes in soil characteristics such as improvement in cation exchange capacity, pH and nutrient contents. This research was developed in collaboration with the landowners within a bottom-up approach. Views of the landowners regarding land management are included in the discussion. Improved management of tropical pasturelands holds opportunity for more sustainable food production and also ecosystem services protection and recuperation, for example, biodiversity net-gain, water regulation and carbon sequestration.
PENGARUH GAYA KEPEMIMPINAN DAN KEPUASAN KERJA TERHADAP PRODUKTIVITAS KERJA PADA PT. MAHA KARYA PUTRA CABANG KABUPATEN PASURUAN
Authors: Yusro Fitri Wakhida , Pujianto Wahyu Eko , Solikhah Afifatus , Supriyadi Supriyadi 
Published: November 2022

Abstrak: Penelitian ini bertujuan untuk mengetahui pengaruh secara simultan maupun secara parsial dari variabel gaya kepemimpinan dan kepuasan kerja terhadap produktivitas karyawan pada PT. Maha Karya Putra Cabang Kabupaten Pasuruan. Metode penelitian ini menggunakan pendekatan kuantitatif. Pengumpulan data dalam penelitian ini diambi melalui kuesioner, dan menggunakan teknik pengukuran Skala likert. Hasil analisis menunjukkan bahwa secara simultan gaya kepemimpinan dan kepuasan kerja berpengaruh positif dan signifikan terhadap produktivitas karyawan dengan nilai F hitung sebesar 4,765 dan nilai F tabel sebesar 3,147. Secara parsial gaya kepemimpinan memiliki nilai sig. 0,022 < 0,05 dan kepuasan kerja memiliki nilai sig. 0,000 < 0,05 hal ini menunjukkan adanya pengaruh yang signifikan terhadap produktivitas karyawan. Diantara variabel bebas terdapat pengaruh yang lebih dominan terhadap produktivitas karyawan pada PT. Maha Karya Putra yaitu kepuasan kerja.
Kata Kunci: Gaya Kepemimpinan, Kepuasan Kerja, Produktivitas Karyawan

Abstract: This study aims to determine the effect simultaneously or partially of leadership style variables and job satisfaction on employee productivity at PT. Maha Karya Putra Pasuruan Regency Branch. The method of this research uses the quantitative approach data collection in this research diambi through the questionnaire, and use measurement technique likert scale. The results of the analysis show that leadership style and job satisfaction simultaneously have a positive and significant effect on employee productivity With a value of count as much as 4,765 and a value of table much as 3,147. Partially the leadership style have value sig. 0,022 < 0,05 and job satisfaction have value sig. 0,000 < 0,05 it show a significant effect on employee productivity. Among the independent variables there is a more dominant influence on employee productivity at PT. Maha Karya Putra is job satisfaction.
Keyword: Leadership Style, Job Satisfaction, Employee Productivity.
Discharge and fate of biocide residuals to ephemeral stormwater retention pond sediments
Authors: Linke Felicia , Olsson Oliver , Schnarr Lena , Kümmerer Klaus , Preusser Frank , Bork Marcus , Leistert Hannes , Lange Jens 
Published: November 2022

Abstract
Biocides used in paints and renders prevent algae and fungi growth but can wash off during wind-driven rain and enter urban environments. Retention ponds represent part of stormwater management that retain water and partly pollutants. However, it is poorly understood which percentage of biocides leached from facades reaches a pond and how efficiently biocides are retained inside ponds although biocides can have harmful environmental effects. Here, we combined measurements and modeling to address diffuse biocide loss and a pond's retention capacity in a delimited residential area of 3 ha, with detached houses connected to an ephemeral retention pond. Six stormwater events were sampled within 2 years and confirmed biocidal residuals at pond inflow. Model results revealed that during the sampled events only 11% of terbutryn leachate arrived at the pond while the major part of this biocide was diffusely lost in the residential area. Measured low terbutryn concentrations in the sediment (mean 2.6 ng g−1) confirmed this result. Model results suggested that approximately 50% of terbutryn reaching the pond were retained and degraded. Our results are site-specific but suggest that biocide retention in ponds is limited, environmental entry pathways are diverse and that biocide use should be limited at its source.
Shared Autonomy to Reduce Sedentary Behavior Among Sit-Stand Desk Users in the United States and India: Web-Based Study
Authors: Kim Lawrence H , Saha Gourab , Leon Annel Amelia , King Abby C , Mauriello Matthew Louis , Paredes Pablo E 
Published: November 2022

Background
Fitness technologies such as wearables and sit-stand desks are increasingly being used to fight sedentary lifestyles by encouraging physical activity. However, adherence to such technologies decreases over time because of apathy and increased dismissal of behavioral nudges.

Objective
To address this problem, we introduced shared autonomy in the context of sit-stand desks, where user input is integrated with robot autonomy to control the desk and reduce sedentary behavior and investigated user reactions and preferences for levels of automation with a sit-stand desk. As demographics affect user acceptance of robotic technology, we also studied how perceptions of nonvolitional behavior change differ across cultures (United States and India), sex, familiarity, dispositional factors, and health priming messages.

Methods
We conducted a web-based vignette study in the United States and India where a total of 279 participants watched video vignettes of a person interacting with sit-stand desks of various levels of automation and answered questions about their perceptions of the desks such as ranking of the different levels of automation.

Results
Participants generally preferred either manual or semiautonomous desks over the fully autonomous option (P<.001). However, participants in India were generally more amenable to the idea of nonvolitional interventions from the desk than participants in the United States (P<.001). Male participants had a stronger desire for having control over the desk than female participants (P=.01). Participants who were more familiar with sit-stand desks were more likely to adopt autonomous sit-stand desks (P=.001). No effects of health priming messages were observed. We estimated the projected health outcome by combining ranking data and hazard ratios from previous work and found that the semiautonomous desk led to the highest projected health outcome.

Conclusions
These results suggest that the shared autonomy desk is the optimal level of automation in terms of both user preferences and estimated projected health outcomes. Demographics such as culture and sex had significant effects on how receptive users were to autonomous intervention. As familiarity improves the likelihood of adoption, we propose a gradual behavior change intervention to increase acceptance and adherence, especially for populations with a high desire for control.
A Linked Open Data–Based Terminology to Describe Libre/Free and Open-source Software: Incremental Development Study
Authors: Jahn Franziska , Ammenwerth Elske , Dornauer Verena , Höffner Konrad , Bindel Michelle , Karopka Thomas , Winter Alfred 
Published: November 2022

BackgroundThere is a variety of libre/free and open-source software (LIFOSS) products for medicine and health care. To support health care and IT professionals select an appropriate software product for given tasks, several comparison studies and web platforms, such as Medfloss.org, are available. However, due to the lack of a uniform terminology for health informatics, ambiguous or imprecise terms are used to describe the functionalities of LIFOSS. This makes comparisons of LIFOSS difficult and may lead to inappropriate software selection decisions. Using Linked Open Data (LOD) promises to address these challenges.ObjectiveWe describe LIFOSS systematically with the help of the underlying Health Information Technology Ontology (HITO). We publish HITO and HITO-based software product descriptions using LOD to obtain the following benefits: (1) linking and reusing existing terminologies and (2) using Semantic Web tools for viewing and querying the LIFOSS data on the World Wide Web.MethodsHITO was incrementally developed and implemented. First, classes for the description of software products in health IT evaluation studies were identified. Second, requirements for describing LIFOSS were elicited by interviewing domain experts. Third, to describe domain-specific functionalities of software products, existing catalogues of features and enterprise functions were analyzed and integrated into the HITO knowledge base. As a proof of concept, HITO was used to describe 25 LIFOSS products.ResultsHITO provides a defined set of classes and their relationships to describe LIFOSS in medicine and health care. With the help of linked or integrated catalogues for languages, programming languages, licenses, features, and enterprise functions, the functionalities of LIFOSS can be precisely described and compared. We publish HITO and the LIFOSS descriptions as LOD; they can be queried and viewed using different Semantic Web tools, such as Resource Description Framework (RDF) browsers, SPARQL Protocol and RDF Query Language (SPARQL) queries, and faceted searches. The advantages of providing HITO as LOD are demonstrated by practical examples.ConclusionsHITO is a building block to achieving unambiguous communication among health IT professionals and researchers. Providing LIFOSS product information as LOD enables barrier-free and easy access to data that are often hidden in user manuals of software products or are not available at all. Efforts to establish a unique terminology of medical and health informatics should be further supported and continued.