bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circular RNA detection identifies circPSEN1 alterations in brain specific to autosomal dominant Alzheimer's disease
Authors: Chen Hsiang-Han , Eteleeb Abdallah , Wang Ciyang , Fernandez Maria Victoria , Budde John P. , Bergmann Kristy , Norton Joanne , Wang Fengxian , Ebl Curtis , Morris John C. , Perrin Richard J. , Bateman Randall J. , McDade Eric , Xiong Chengjie , Goate Alison , Farlow Martin , Chhatwal Jasmeer , Schofield Peter R. , Chui Helena , Harari Oscar , Cruchaga Carlos , Ibanez Laura ,   Dominantly Inherited Alzheimer Network
Published: March 2022

AbstractBackgroundAutosomal-dominant Alzheimer's disease (ADAD) is caused by pathogenic mutations inAPP,PSEN1, andPSEN2, which usually lead to an early age at onset (< 65). Circular RNAs are a family of non-coding RNAs highly expressed in the nervous system and especially in synapses. We aimed to investigate differences in brain gene expression of linear and circular transcripts from the three ADAD genes in controls, sporadic AD, and ADAD.MethodsWe obtained and sequenced RNA from brain cortex using standard protocols. Linear counts were obtained using the TOPMed pipeline; circular counts, using python package DCC. After stringent quality control (QC), we obtained the counts forPSEN1,PSEN2andAPPgenes. Only circPSEN1passed QC. We used DESeq2 to compare the counts across groups, correcting for biological and technical variables. Finally, we performedin-silicofunctional analyses using the Circular RNA interactome website and DIANA mirPath software.ResultsOur results show significant differences in gene counts of circPSEN1in ADAD individuals, when compared to sporadic AD and controls (ADAD = 21, AD = 253, Controls = 23—ADADvsCO: log2FC = 0.794,p = 1.63 × 10–04, ADADvsAD: log2FC = 0.602,p = 8.22 × 10–04). The high gene counts are contributed by two circPSEN1species (hsa_circ_0008521 and hsa_circ_0003848). No significant differences were observed in linearPSEN1gene expression between cases and controls, indicating that this finding is specific to the circular forms. In addition, the high circPSEN1levels do not seem to be specific toPSEN1mutation carriers; the counts are also elevated in APP andPSEN2mutation carriers.In-silicofunctional analyses suggest that circPSEN1is involved in several pathways such as axon guidance (p = 3.39 × 10–07), hippo signaling pathway (p = 7.38 × 10–07), lysine degradation (p = 2.48 × 10–05) or Wnt signaling pathway (p = 5.58 × 10–04) among other KEGG pathways. Additionally, circPSEN1counts were able to discriminate ADAD from sporadic AD and controls with an AUC above 0.70.ConclusionsOur findings show the differential expression of circPSEN1is increased in ADAD. Given the biological function previously ascribed to circular RNAs and the results of ourin-silicoanalyses, we hypothesize that this finding might be related to neuroinflammatory events that lead or that are caused by the accumulation of amyloid-beta.
An ontological data model for points of interest (POI) in a cultural heritage site
Authors: Ranjgar Babak , Sadeghi-Niaraki Abolghasem , Shakeri Maryam , Choi Soo-Mi 
Published: March 2022

Abstract
Cultural heritage (CH) reflects on the history of a society and its traditions and it is treated as the nation’s memory and identity. Digitizing and web, beside its benefits, brought some challenges in disseminating and retrieving CH information, which has heterogeneous content varying widely in type and properties yet encompassing rich semantic links. Semantic web technologies, especially ontologies, provide a common understanding inside a domain that helps sharing knowledge and interoperability. They can be very helpful in data modeling for a better information retrieval compared to relational databases as they take into account the semantics of information, guarantee reusability, and make information machine-readable that can offer more flexibility to intelligent services and applications. CH community is one of the first domains to make use semantic web technologies to deal with this issue. CIDOC CRM is the most used and famous ontology in CH domain, which is an ISO standard since 2006. Heritage sites are composed of many points of interest that attract visitors to find out about them. However, information about a particular POI is complex and interconnected with other people, events, and objects. In this paper, we aim to develop a POI-based data model for heritage sites in Iran using concepts from CIDOC CRM integrated with GeoSPARQL, the standard ontology in geospatial field, to incorporate spatial semantics with heritage information. This way the user can freely explore their preferred information about the places they desire. This can make it possible to use the data model for location-based services and applications in heritage sites.
Which evidence-based teaching practices change over time? Results from a university-wide STEM faculty development program
Authors: Jackson Mallory A. , Moon Sungmin , Doherty Jennifer H. , Wenderoth Mary Pat 
Published: March 2022

AbstractBackgroundThere is overwhelming evidence that evidence-based teaching improves student performance; however, traditional lecture predominates in STEM courses. To provide support as faculty transform their lecture-based classrooms with evidence-based teaching practices, we created a faculty development program based on best practices, Consortium for the Advancement of Undergraduate STEM Education (CAUSE). CAUSE paired exploration of evidence-based teaching with support for classroom implementation over two years. Each year for three years, CAUSE recruited cohorts of faculty from seven STEM departments. Faculty met biweekly to discuss evidence-based teaching and receive feedback on their implementation. We used the PORTAAL observation tool to document evidence-based teaching practices (PORTAAL practices) across four randomly chosen class sessions each term. We investigated if the number of PORTAAL practices used or the amount of practices increased during the program.ResultsWe identified identical or equivalent course offerings taught at least twice by the same faculty member while in CAUSE (n = 42 course pairs). We used a one-way repeated measures within-subjects multivariate analysis to examine the changes in average use of 14 PORTAAL practices between the first and second timepoint. We created heat maps to visualize the difference in number of practices used and changes in level of implementation of each PORTAAL practice. Post-hoc within-subjects effects indicated that three PORTAAL practices were significantly higher and two were lower at timepoint two. Use of prompting prior knowledge and calling on volunteers to give answers decreased, while instructors doubled use of prompting students to explain their logic, and increased use of random call by almost 40% when seeking answers from students. Heat maps indicated increases came both from faculty’s adoption of these practices and increased use, depending on the practice. Overall, faculty used more practices more frequently, which contributed to a 17% increase in time that students were actively engaged in class.ConclusionsResults suggest that participation in a long-term faculty development program can support increased use of evidence-based teaching practices which have been shown to improve student exam performance. Our findings can help prioritize the efforts of future faculty development programs.
Patellofemoral arthroplasty: expert opinion
Authors: Hoogervorst Paul , Arendt Elizabeth A. 
Published: March 2022

AbstractIsolated patellofemoral osteoarthritis (PFOA) is a common cause of anterior knee pain in patients over the age of 40 years. Patellofemoral arthroplasty (PFA) is an option to address PFAO when the non-operative or joint preserving management has failed.The goals of PFA are to reduce pain and increase function of the knee in a bone and ligament preserving fashion while maintaining or optimizing its kinematics. Over the last decades advances have been made in optimizing implants designs, addressing complications and improving functional and patient reported outcomes. Appropriate patient selection has proven to be imperative. Proper surgical technique and knowledge of pearls and pitfalls is essential.The indications and surgical technique for patellofemoral arthroplasty will be reviewed here.Level of evidence: Therapeutic Level V.
Assessment of the obesogenic environment in primary schools: a multi-site case study in Jakarta
Authors: Khoe Levina Chandra , Widyahening Indah Suci , Ali Syougie , Khusun Helda 
Published: March 2022

Abstract
Background
Childhood overweight and obesity have increasingly been recognized as a significant global public health crisis, including in Asia. This study aimed to assess the obesogenic environment in primary schools in Jakarta, Indonesia.

Methods
A qualitative, multi-site, case study design was used to capture different elements of the school environment and policies related to obesity, with a focus on nutrition and physical activity. An adaptation of the Primary School Environmental Assessment tool was used. Six primary schools in Jakarta were purposively selected based on their location, socioeconomic status, and type (public or private). In addition to direct observation at each school, interviews were conducted with the principal, physical education teacher, canteen staff, street food vendors, and students.

Results
Among the six schools, two were private and four were public. The most popular foods consumed by students were unhealthy, such as deep-fried foods and sugar-sweetened beverages. Students had easy and constant access to unhealthy foods, whereas only limited variation of healthy foods were available in the school canteen. Some schools also allowed the student to have access to street food vendors. School policies related to healthy eating and physical activities had been implemented, mainly in the form of teaching these topics as part of the school curriculum. However, promotion of healthy eating and physical activities by the schools was still limited.

Conclusions
This study showed the usefulness of the Primary School Environmental Assessment tool in identifying obesogenic factors in urban area of Indonesia. Effective implementation of guidelines to foster good nutritional practices and healthy lifestyles at school should be prioritized to improve the health and nutritional status of the students.
Retinal and choroidal thickness in pediatric patients with sickle cell disease: a cross-sectional cohort study
Authors: Prazeres Juliana , Lucatto Luiz Filipe , Ferreira Adriano , Moraes Nilva , Braga Josefina A. P. , Lima Luiz H. , Regatieri Caio , Maia Maurício 
Published: March 2022

Abstract
Background
To measure the retinal/choroidal thicknesses in the macular area of asymptomatic pediatric patients with sickle cell disease (SCD).

Methods
This cross-sectional cohort study included 40 children (79 eyes) with SCD and 19 control patients (36 eyes). All subjects underwent spectral-domain optical coherence tomography (SD-OCT) with enhanced-depth imaging OCT. Generalized Estimating Equations (GEE) were applied to compare the outcomes between groups. P ≤ 0.05 was considered significant.

Results
The choroidal thickness in the macular area in the study subfields was significantly thinner in the SCD eyes compared with control eyes (subfoveal subfield and temporal parafoveal subfield, p < 0.0001; nasal parafoveal subfield, p < 0.0001 temporal perifoveal subfield, p < 0.0001; and nasal perifoveal subfield, p < 0.0001). The variations in the retinal thickness were not significant.

Conclusion
EDI-OCT showed that the macular choroidal thickness is thinner in asymptomatic pediatric patients with SCD.
Microbiome structure in large pelagic sharks with distinct feeding ecologies
Authors: Pratte Zoe A. , Perry Cameron , Dove Alistair D. M. , Hoopes Lisa A. , Ritchie Kim B. , Hueter Robert E. , Fischer Chris , Newton Alisa L. , Stewart Frank J. 
Published: March 2022

Abstract
Background
Sharks play essential roles in ocean food webs and human culture, but also face population declines worldwide due to human activity. The relationship between sharks and the microbes on and in the shark body is unclear, despite research on other animals showing the microbiome as intertwined with host physiology, immunity, and ecology. Research on shark-microbe interactions faces the significant challenge of sampling the largest and most elusive shark species. We leveraged a unique sampling infrastructure to compare the microbiomes of two apex predators, the white (Carcharodon carcharias) and tiger shark (Galeocerdo cuvier), to those of the filter-feeding whale shark (Rhincodon typus), allowing us to explore the effects of feeding mode on intestinal microbiome diversity and metabolic function, and environmental exposure on the diversity of microbes external to the body (on the skin, gill).

Results
The fecal microbiomes of white and whale sharks were highly similar in taxonomic and gene category composition despite differences in host feeding mode and diet. Fecal microbiomes from these species were also taxon-poor compared to those of many other vertebrates and were more similar to those of predatory teleost fishes and toothed whales than to those of filter-feeding baleen whales. In contrast, microbiomes of external body niches were taxon-rich and significantly influenced by diversity in the water column microbiome.

Conclusions
These results suggest complex roles for host identity, diet, and environmental exposure in structuring the shark microbiome and identify a small, but conserved, number of intestinal microbial taxa as potential contributors to shark physiology.
Submillisievert CT chest for COVID-19 patients in a rural hospital with limited resources
Authors: Tawk Sammy , Mansour Wissam , Sleiman Dayana , Gemayel Setrida , Lozom Edgard , El Mendelek Karl , Saliba Nicole , Mourad Charbel 
Published: March 2022

Abstract
Background
This is a secondary analysis of prospectively acquired data approved by the hospital institutional board committee. We performed a retrospective chart review of 463 patients who underwent a CT Chest for suspected COVID-19 infection between April 1st, 2020, and March 31st, 2021. Patients were grouped based on the CT chest obtained protocol: ultra-low dose or full dose. The likelihood of suspicion of COVID-19 infection was classified on a Likert scale based on the probability of pulmonary involvement. For each group, the sensitivity and specificity of CT were compared to nasopharyngeal swab as standard of reference. The median dose length product and duration of apnea were compared between both groups using two-tailed Mann–Whitney U test. The aim of this study is to share our experience of reducing radiation dose in COVID-19 patients by using an ultra-low dose CT chest protocol on a 16 row multidetector CT scan in a hospital with limited resources.

Results
Two hundred sixty-nine patients underwent a full dose CT and 194 patients an ultra-low dose CT. In the former group, the median dose length product was 341.11 mGy*cm [Interquartile range (IQR), 239.1–443.2] and the median duration of apnea was 13.29 s [IQR, 10.85–15.73]. In the latter group, the median dose length product was 30.8 mGy*cm [IQR, 28.9–32.7] and median duration of apnea was 8.27 s [IQR, 7.69–8.85]. The sensitivity of the ultra-low dose CT was 91.2% and that of the full dose was 94%.

Conclusion
A 90% reduction in estimated dose and 38% reduction in apnea duration could be achieved using an ultra-low dose CT chest protocol on a 16-row MDCT without significant loss in the sensitivity of CT to detect COVID-related parenchymal involvement.
Coordinated control of DSTATCOM with switchable capacitor bank in a secondary radial distribution system for power factor improvement
Authors: Rafi K. Mahammad , Prasad P. V. N. , Vithal J. V. R. 
Published: March 2022

AbstractThis paper exhibits the coordinated control of 30 kVAr Distribution STATic synchronous COMpensator (DSTATCOM) with 125 kVAr Switchable Capacitor Banks for compensation of reactive power in a 750 kVA secondary radial distribution system. With the control of reactive power in a radial distribution system, the power factor can be improved near to unity. The selected radial distribution system mainly feeding power to vital loads of an Educational Institution. In this paper, the study of 750 kVA secondary radial distribution system is analyzed in terms of electrical power system of institute, power consumption pattern and tariff related issues. Some conclusions to improve the system performance in terms of power factor and reduction in tariff were drawn. The coordinated control of switchable capacitor bank and DSTATCOM performance depends on the calculation of the reference source currents that generates the gating pulses of the voltage source converter-based DSTATCOM. For this purpose, the control strategy adopted is Real and Reactive power (PQ) control, Synchronous Reference Frame theory, Back Propagation Control algorithm and Adaptive Linear (ADALINE) control is implemented in this system using MATLAB/SIMULINK software. Generation of the PWM pulses triggers the IGBT of the VSI-based DSTATCOM. This is achieved using DSP TMS 320 F 2812, a 32-bit processor that is programmed with CCS V3.3 and C2000 embedded code generation tool using MATLAB/Simulink, and the same is being executed with code composer studio V 6.0.1. The performance of the selected secondary radial distribution system is analyzed experimentally in a hardware prototype to evaluate the effect of DSTATCOM and switchable capacitor bank.
Genebanks and market participation: evidence from groundnut farmers in Malawi
Authors: Tabe-Ojong Martin Paul , Smale Melinda , Jamora Nelissa , Azevedo Vania 
Published: March 2022

Abstract
Background
Genebanks contribute to poverty reduction as well as food and nutritional security by being one of the main sources of diversity for the development of improved crop varieties. While the welfare implications of adopting improved varieties have been documented in many rural settings, little attention has been placed on genebanks that often supply key traits and genetic diversity to plant breeders by providing seed samples. In this study, we examined the contribution of the genebank housed by the International Crops Research Institute (ICRISAT) to the development of improved groundnut varieties used by farmers in Malawi. We then related this apportioned genebank contribution to market outcomes, such as market participation and the quantity of groundnut sold in markets.

Methods
Pedigree data obtained through consultations with genebank scientists and breeders were used in combination with a three-wave balanced household-level panel dataset of 447 smallholder farmers in Malawi. Different econometric techniques were used, including a double hurdle model to understand market participation and quantity of groundnuts sold.

Results
We found households to be using six improved groundnut varieties, four of which were traced to the ICRISAT genebank. We analyzed pedigrees of the varieties and apportioned the ancestral contribution of the genebank accessions. Linking the improved varieties grown by farmers with genebank ancestry to market outcomes, we observed a positive association between the ICRISAT genebank and market participation. We could not establish a robust effect on the quantity of groundnuts sold conditional on participation. We found the results to be driven by the area under improved groundnuts.

Conclusion
The ICRISAT genebank has provided accessions that confer useful traits to improved varieties of groundnut adopted by farmers in Malawi. Our analysis indicates that access to genetic resources from genebanks has resulted in the development of improved varieties with traits that are preferred by farmers such as higher yields and resistance to diseases. The adoption of these improved varieties led to increased production surplus and reduced transaction costs, allowing farmers to better participate in local groundnut markets. The study points to the crucial role of genebanks as important sources of crop diversity for improved food security and incomes of smallholder farmers.
Therapeutic progress and challenges for triple negative breast cancer: targeted therapy and immunotherapy
Authors: Yang Ruoning , Li Yueyi , Wang Hang , Qin Taolin , Yin Xiaomeng , Ma Xuelei 
Published: March 2022

AbstractTriple negative breast cancer (TNBC) is a subtype of breast cancer, with estrogen receptor, human epidermal growth factor receptor 2 and progesterone receptor negative. TNBC is characterized by high heterogeneity, high rates of metastasis, poor prognosis, and lack of therapeutic targets. Now the treatment of TNBC is still based on surgery and chemotherapy, which is effective only in initial stage but almost useless in advanced stage. And due to the lack of hormone target, hormonal therapies have little beneficial effects. In recent years, signaling pathways and receptor-specific targets have been reported to be effective in TNBC patients under specific clinical conditions. Now targeted therapies have been approved for many other cancers and even other subtypes of breast cancer, but treatment options for TNBC are still limited. Most of TNBC patients showed no response, which may be related to the heterogeneity of TNBC, therefore more effective treatments and predictive biomarkers are needed. In the present review, we summarize potential treatment opinions for TNBC based on the dysregulated receptors and signaling pathways, which play a significant role in multiple stages of TNBC development. We also focus on the application of immunotherapy in TNBC, and summarize the preclinical and clinical trials of therapy for patients with TNBC. We hope to accelerate the research and development of new drugs for TNBC by understanding the relevant mechanisms, and to improve survival.