bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive optical quantitative phase imaging based on annular illumination Fourier ptychographic microscopy
Authors: Shu Yefeng , Sun Jiasong , Fan Yao , Zhou Ning , Ye Ran , Zheng Guoan , Chen Qian , Zuo Chao 
Published: August 2022

Abstract
Quantitative phase imaging (QPI) has emerged as a valuable tool for biomedical research thanks to its unique capabilities for quantifying optical thickness variation of living cells and tissues. Among many QPI methods, Fourier ptychographic microscopy (FPM) allows long-term label-free observation and quantitative analysis of large cell populations without compromising spatial and temporal resolution. However, high spatio-temporal resolution imaging over a long-time scale (from hours to days) remains a critical challenge: optically inhomogeneous structure of biological specimens as well as mechanical perturbations and thermal fluctuations of the microscope body all result in time-varying aberration and focus drifts, significantly degrading the imaging performance for long-term study. Moreover, the aberrations are sample- and environment-dependent, and cannot be compensated by a fixed optical design, thus necessitating rapid dynamic correction in the imaging process. Here, we report an adaptive optical QPI method based on annular illumination FPM. In this method, the annular matched illumination configuration (i.e., the illumination numerical aperture (NA) strictly equals to the objective NA), which is the key for recovering low-frequency phase information, is further utilized for the accurate imaging aberration characterization. By using only 6 low-resolution images captured with 6 different illumination angles matching the NA of a 10x, 0.4 NA objective, we recover high-resolution quantitative phase images (synthetic NA of 0.8) and characterize the aberrations in real time, restoring the optimum resolution of the system adaptively. Applying our method to live-cell imaging, we achieve diffraction-limited performance (full-pitch resolution of 655 nm at a wavelength of 525 nm across a wide filed of view (1.77 mm 2 ) over an extended period of time.
Diversify Your Faculty: A Roadmap for Equitable Hiring Strategies
Authors: Cosgriff-Hernandez Elizabeth , Aguado Brian , Akpa Belinda , Fleming Gabriella Coloyan , Moore Erika , Porras Ana Maria , Boyle Patrick , Chan Deva , Chesler Naomi , Christman Karen , Desai Tejal , Harley Brendan , Killian Megan , Maisel Katharina , Maitland Kristen , Peyton Shelly , Pruitt Beth , Stabenfeldt Sarah , Stevens Kelly , Bowden Audrey 
Published: August 2022

Abstract
Hiring practices in academia have critically limited the entry of individuals from historically excluded groups (e.g., people who identify as Black/African American, Hispanic/Latino, American Indian/Alaskan Native, LGBTQ+, people with disabilities) into our biomedical engineering faculty. Excluding such individuals has hindered our profession’s research impact and ability to equitably educate our students. With many departments committed to “do better,” we now need to embrace a new mindset and gain the skills necessary to rectify injustices in our faculty hiring processes. Here, we offer a faculty hiring roadmap that departments can leverage to eliminate many barriers of entry to members of historically excluded groups as faculty in biomedical engineering. We call on our colleagues to recognize the failings of our current hiring practices and adopt the guidelines provided here to diversify biomedical engineering departments so that we might collectively accelerate the impact, innovation, and power of our profession.
The effect of high throughput vitrification of human ovarian cortex tissue on follicular viability. A promising alternative to conventional slow freezing ?
Authors: Schallmoser Andreas , Einenkel Rebekka , Färber Cara , Emrich Norah , John Julia , Sänger Nicole 
Published: August 2022

Abstract
Background: The standard procedure most frequently used for ovarian tissue cryopreservation (OTC) is slow freezing, while vitrification has been proposed as promising alternative and has built an impressive catalogue of success in fertility laboratories regarding cryopreservation of oocytes and embryos. Methods: We developed and evaluated a high throughput protocol for vitrification of human ovarian tissue suitable for clinical processing. Follicular viability was assessed via calcein staining prior and after cryopreservation analysing ovarian tissue of a cohort of 30 patients. Results: We found no significant differences regarding follicular viability between slow frozen and vitrified cortex tissue samples 24 h after thawing and rapid warming. Follicular viability of thawed and rapid warmed samples was not significantly different in comparison to fresh samples, indicating high proportions of follicular survival rates with both methods. Conclusions: High throughput vitrification is a promising option in a clinical setting. More research is needed to determine the status of other tissue specific quality indicators potentially influencing on autotransplantation.
Exploring the anticancer activity of five Hyalomma species (Acari: Ixodidae) salivary gland extracts on human colorectal cancer cell line HT-29
Authors: Tavassoli Maryam , Kadivar Mehdi , Akhavan Amir Ahmad , Abdi-goudarzi Mohammad , Chaibakhsh Samira , Beik-mohammadi Mojtaba , Sedaghat Mohammad Mehdi 
Published: August 2022

Abstract
The authors have requested that this preprint be removed from Research Square.
High reproducibility of a novel fixed anterior drawer test for diagnosing ankle instability
Authors: Murahashi Yasutaka , Teramoto Atsushi , Takahashi Katsunori , Okada Yohei , Okimura Shinichiro , Imamura Rui , Kawai Makoto , Watanabe Kota , Yamashita Toshihiko 
Published: August 2022

Abstract
BackgroundThe manual traditional anterior drawer test (ADT) is essential for deciding the treatment for chronic ankle instability, but it has been shown to have a comparatively low reproducibility and accuracy, especially in less experienced hands. To clarify the inter-examiner reproducibility, we compared the actual distance of anterior translation between junior and senior examiners in ADT. We also evaluated the diagnostic abilities of traditional ADT, and a novel modified ADT (fixed ADT).MethodsThirty ankles were included in this study, and ankle instability was defined using stress radiography. All subjects underwent two methods of manual ADT by junior and senior examiners, and ankle instability was judged in a blinded fashion. The anterior drawer distance was calculated from the lengthening measured using a capacitance-type sensor device. ResultsThe degree of anterior translation determined by the junior examiner was significantly lower than that determined by the senior examiner when traditional ADT was performed (3.3 vs. 4.5 mm, P=0.016), but there was no significant difference in anterior translation between the two examiners when fixed ADT was performed (4.6 vs. 4.1 mm, P=0.168). The inter-examiner reliability of fixed ADT was higher than that of traditional ADT. For the junior examiner, the diagnostic accuracy of fixed ADT was higher than that of traditional ADT (sensitivity, 0.40 vs. 0.80; specificity, 0.75 vs. 0.80).ConclusionFixed ADT may have the advantage of being a simple manual test of ankle instability with less error between examiners.
Genomic adaptation to extreme climate conditions in beef cattle as a consequence of cross-breeding program
Authors: Tian Rugang , Nanaie Hojjat Asadollahpour , Wang Xiao , Zhao Meng , Wang Fenf , Li Hui , Yang Ding , Zhang Hao , Li SuFan , Li Yuan , Luan Tu 
Published: August 2022

Abstract
BackgroundUnderstanding the evolutionary forces related to climate changes that have been shaped genetic variation within species has long been a fundamental pursuit in biology. In this study, we generated whole-genome sequence (WGS) data from 65 cross-bred and 45 Mongolian cattle breeds. Together with 61 whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of cattle populations. In addition, we performed comparative population genomics analyses to explore the genetic basis underlying variation in the adaptation to cold climate and immune response in cross-bred cattle located in the cold region of China. To elucidate genomic signatures that underlie adaptation to cold climate, we performed statistical measurements, FST and nucleotide diversity (θπ), and further investigated the results to identify genomic regions under selection for cold adaptation and immune response-related traits.ResultsBy generating whole-genome sequencing data, we first investigated the population genetic structure and phylogenetic relationship of studied cattle populations. The results revealed clustering of cattle groups in agreement with their geographic distribution. We detected noticeable genetic diversity between indigenous cattle ecotypes and commercial populations. Analysis of population structure demonstrated evidence of shared genetic ancestry between studied cross-bred population and both Red-Angus and Mongolian breeds. Among the all studied cattle populations, the highest and lowest levels of linkage disequilibrium (LD) were detected in Holstein and Rashoki populations (ranged from ~ 0.54 to 0.73, respectively) at marker pairs distance of 1 Kb. Our search for potential genomic regions under selection in cross-bred cattle revealed several candidate genes related with immune response and cold shock protein-related traits. In particular, we identified some adaptive introgression genes such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis. In addition, we detected some candidate genes on different chromosomes probably associated with immune response-related traits. ConclusionsThe study identified candidate genes involved in responses to cold adaptation and immune response in cross-bred cattle, including new genes or gene pathways putatively involved in these adaptations. The identification of these genes may be helpful in understanding of the molecular basis of adaptation to extreme environmental climate and as such they should be used in cattle breeding programs to select more efficient breeds for cold climate regions.
First zootiological survey of Amblyomma geoemydae ticks (Acari: Ixodidae) infesting wild turtles in Northern Taiwan
Authors: Chao Li-Lian , Chen Tien-Hsi , Shih Chien-Ming 
Published: August 2022

Abstract
The prevalence of Amblyomma geoemydae infesting wild turtles (Cuora flavomarginata) was determined for the first time in northern Taiwan. A total of 352 ticks including 140 adults, 61 nymphs and 151 larvae were collected from 56 wild turtles. The overall infestation was observed with an average density of 6.29 ticks per turtle and the highest seasonal prevalence was observed on March with an average tick density of 14.25 ticks per turtle. The higher seasonal prevalence was observed on April, May, July and October with an average density of 4.82, 8.33, 5.67 and 8.50 ticks per turtle, respectively. The genetic identity was determined by comparing the sequences of ITS2 genes obtained from 7 Taiwan strains of Am. geoemydae and 9 other strains representing 8 species of Amblyomma and 1 outgroup species of Ixodes tick. Our results provide the first zootiological survey of Am. geoemydae ticks infesting wild turtles in northern Taiwan and highlight the possible geographical impacts of this tick species on animal/human health.
Immunomodulatory effect of kainic acid on HMGB1/TLR4 pathway in a thalamic reticular nucleus slice seizure model in rats
Authors: Li Dongbin , Zhang Xiaosi , Liu Ruoshi , Long Meixin , Zhou Shanshan , Lin Jinghan , Zhang Liming 
Published: August 2022

Abstract
Objective: To explore the relationship between pro-inflammatory factor high-mobility group box 1 (HMGB1) and glutamatergic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in the development of epilepsy. Methods: Thalamic reticular nucleus (TRN) slice was treated with kainic acid (KA) to simulate seizure. Seizure-like spikes and spontaneous inhibitory postsynaptic currents (sIPSCs) were recorded within TRN slices using whole-cell patch clamp techniques. The translocation of HMGB1 were detected by Immunofluorescence. HMGB1/TLR4 signaling pathway and its downstream inflammatory factors (IL-1β and NF-κB) were detected by RT-PCR, Western blot and ELISA. Results: KA-evoked seizure-like spikes were observed in the TRN slices and blocked by perampanel. sIPSCs in the TRN were enhanced by KA and blocked by perampanel. The translocation of HMGB1 in TRN were promoted by KA and inhibited by perampanel. The expression of HMGB1/TLR4 signaling pathway were promoted by KA and suppressed by perampanel. Conclusion: The AMPA receptor and HMGB1/TLR4 signaling pathway interaction jointly contribute to the development of epilepsy.
Energy Efficient Congestion Control Scheme for Wireless Sensor Networks using Adaptive Neuro Fuzzy Inference System with Black Widow Optimization
Authors: Ali Abdul , Vadivel M. 
Published: August 2022

Abstract
Network congestion is one of the major issues in wireless sensor networks (WSNs) that result in packet loss, reduced network lifetime, low throughput and energy waste. Determining a better path to mitigate the congestion is a better approach to improve the performance of WSNs. In this paper, an adaptive neuro-fuzzy inference system (ANFIS) based path determination approach is proposed to mitigate the congestion with black widow optimization (BWO) algorithm. The hop count, buffer occupancy and remaining energy are considered as the input factors for the ANFIS. The simulation results of the proposed method show better quality of service, high energy, low delay, high packet delivery ratio with number of increasing alive nodes when compared to existing methods.
Immigrant and Refugee Experiences of Healthcare Access and Wellbeing During Covid-19 in Vermont: A Qualitative Evaluation
Authors: Velez Christine M. , Ávila Maria Mercedes , Darivemula Shilpa , Cavoretta Thomas E. 
Published: August 2022

Abstract
Background
Refugee and immigrant communities all over the world have been historically underserved in health and social services and more negatively impacted by policies meant to address crisis rather than focusing on preventive care and culturally sensitive services. The lack of culturally responsive services coupled with systemic discrimination faced by refugee and immigrant populations are amplified during the Covid-19 pandemic. Perspectives from refugee and immigrant groups are often lacking in the published literature. This qualitative evaluation includes focus groups with five distinct refugee and immigrant communities who shared perspectives on their experiences accessing healthcare during the Covid-19 pandemic in Vermont.
Methods
A total of 114 participants who identify as refugees and/or immigrants, and who reside in Vermont, participated in 10 focus groups representing the following five different cultural groups of refugees and immigrants: Nepali/Bhutanese, Congolese, Somali/Somali Bantu, Burmese and Arabic. Cultural brokers or community case managers helped recruit participants and assisted in the focus groups providing interpretation and translation services. Focus groups took place remotely via online platforms. Although focus groups were conducted in English, interpreters were present and focus group guides were translated to the languages spoken by the aforementioned groups. Focus groups were audio recorded and transcribed with patient confidentiality maintained. Four themes were identified through a process of thematic analysis as identified by Braun and Clarke.
Results
Participants encountered several challenges in having meaningful interactions with health care providers and found it difficult to schedule appointments. Interpretation and translation services were also sporadic and inadequate. Interpretation was most reliable via Telehealth and Zoom calls, yet most participants did not experience this as an ideal format for health care. Participants shared their experiences with Covid testing and vaccination. Although some reported positive experiences, many participants communicated barriers in the process and shared experiences of discrimination. Although vaccine hesitancy was expressed by some participants, some also felt eager and hopeful about the Covid-19 vaccine.
Conclusions
Refugee and immigrant participants encountered many challenges in accessing health care during the Covid-19 pandemic. Discussions with the community and trusted cultural brokers created space for shared solutions and patient-driven ideas for care improvement.
The development of an optimized and reliable iron overload HepG2 cell model
Authors: Abbasi Usama , Abbina Srinivas , Kizhakkedathu Jayachandran N. 
Published: August 2022

Abstract
Cell-based iron overload models provide tremendous utility for the investigations into the pathogenesis of different diseases as well as assessing efficacy of various therapeutic strategies. In the literature, establishing such models vary tremendously with regards to cell lines, iron source, iron treatment conditions and duration. Due to this diversity, researchers reported significant differences in the measured outcomes, either in cellular function or response to a stimulus. Herein, we report the process required to establish an iron overload HepG2 cell model to achieve a consistent and reproducible results such that the literature can strive towards a consensus. Iron loading in cells was achieved with 50 µM of iron every 24 hours for 2 days, followed by an additional 24 hours of maintenance in fresh media. We demonstrated that iron overloaded cells had significantly increased ROS generation, labile and total iron whilst having various cellular functions resemble cells without iron overload. The present report addresses key pitfalls with regards to the lack of consensus currently present in the literature.
The value of artificial intelligence for detection and grading of prostate cancer in human prostatectomy specimens: a validation study
Authors: Kudo Maíra Suzuka , Souza Vinicius Meneguette Gomes , Estivallet Carmen Liane Neubarth , Amorim Henrique Alves , Kim Fernando J. , Leite Katia Ramos Moreira , Moraes Matheus Cardoso 
Published: August 2022

Abstract
Background
The Gleason grading system is an important clinical practice for diagnosing prostate cancer in pathology images. However, this analysis results in significant variability among pathologists, hence creating possible negative clinical impacts. Artificial intelligence methods can be an important support for the pathologist, improving Gleason grade classifications. Consequently, our purpose is to construct and evaluate the potential of a Convolutional Neural Network (CNN) to classify Gleason patterns.
Methods
The methodology included 6982 image patches with cancer, extracted from radical prostatectomy specimens previously analyzed by an expert uropathologist. A CNN was constructed to accurately classify the corresponding Gleason. The evaluation was carried out by computing the corresponding 3 classes confusion matrix; thus, calculating the percentage of precision, sensitivity, and specificity, as well as the overall accuracy. Additionally, k-fold three-way cross-validation was performed to enhance evaluation, allowing better interpretation and avoiding possible bias.
Results
The overall accuracy reached 98% for the training and validation stage, and 94% for the test phase. Considering the test samples, the true positive ratio between pathologist and computer method was 85%, 93%, and 96% for specific Gleason patterns. Finally, precision, sensitivity, and specificity reached values up to 97%.
Conclusion
The CNN model presented and evaluated has shown high accuracy for specifically pattern neighbors and critical Gleason patterns. The outcomes are in line and complement others in the literature. The promising results surpassed current inter-pathologist congruence in classical reports, evidencing the potential of this novel technology in daily clinical aspects.
Peroxiredoxin 4 in alveolar macrophages: a novel target for the treatment of silicosis fibrosis
Authors: Zhou Jiawei , Bai Ying , Guo Jianqiang , Liu Yafeng , Zhang Xin , Liang Chao , Wang Wenyang , Xing Yingru , Wu Jing , Hu Dong 
Published: August 2022

Abstract
Silicosis is an occupational disease with the highest morbidity and mortality, and no specific medicine or recognized cure is available. Here, for the first time, we identified peroxiredoxin 4 (PRDX4) as a tissue-specific regulator of alveolar macrophages (AMs) in silicosis patients. We construct mouse models of early silicosis with self-repair and silicosis with systemic inhibition or conditional knockdown of PRDX4. Mechanistically, PRDX4 is selectively and highly expressed in AMs of silicosis patients and mice, which activates AMs through AKT/NF-κB pathway, thus promoting the transformation of pulmonary epithelial cells and fibroblasts. Functionally, systemic administration of a PRDX4 inhibitor (Conoidin A) significantly improves pulmonary self-repair in early silicosis mice. Interestingly, when knocking down PRDX4 of AMs by AAV virus vector, it not only prominently prevents the progression of crystalline silica (CS)-induced pulmonary fibrosis in mice, but also exhibits lower side effects. Taken together, these findings highlight PRDX4 as a novel target of AMs in regulating pulmonary inflammation and fibrosis, and targeted inhibition of PRDX4 in AMs may support a potential therapeutic strategy for silicosis.
A storm in a teacup: Exchange, prices, and credits.
Authors: Avetisyan Sergey 
Published: August 2022

Abstract
The one of most popular tools for measuring online behavior is Google Trends, an open tool that provides information on trends and the variations of online interest in selected keywords and topics over time. In this paper I show some stylised facts about economic activities like exchange, prices, and credits, from non official statistics. I use Google Trend data for measuring this words searching as proxy of financial actions determinants in Republic of Armenia. I use the Holt-Winters model for predict the patterns of people searches for exchange, prices, and credit over a given time interval.JEL classification: C22, C32, C5.