jimnoneill/paper-to-field-training huggingface dataset:
Current Trends in VCO-Based EPR

Field: Engineering (Physical Sciences)

Abstract In this article we provide an overview of chip-integrated voltage-controlled oscillator (VCO)-based EPR detection as a new paradigm in EPR sensing. After a brief motivation for this alternative detection method, we provide a self-contained overview of the detection principle, both for continuous-wave and pulsed detection. Based on this introduction, we will highlight the advantages and disadvantages of VCO-based detection compared to conventional resonator-based detection. This is followed by an overview of the current state of the art in VCO-based EPR and interesting emerging applications of the technology. The paper concludes with a brief summary and outlook on future research directions.
PHILIPPINE ETHNOBOTANICALS DOWNREGULATE lasR EXPRESSION LINKED TO QUORUM SENSING-MEDIATED BIOFILM FORMATION IN Pseudomonas aeruginosa

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

The prevalence of antibacterial resistance has brought about a growing surge to develop novel approaches to control infectious diseases. Targeting Quorum-sensing (QS) - controlled virulence factors in bacteria has indicated a promising strategy for antipathogenic drugs. Extracts of Philippine Ilongot-Egongot ethnobotanicals Stachytarpeta jamaicensis, Adenanthera intermedia, Mikania micrantha, Hyptis suaveolens, Premna odorata, Cymbopogan winterianus, Phyllanthus urinaria, Dillenia philippinensis, Hydrocotyle vulgaris, Senna alata, Urena lobata, Ceiba pentandra, Ficus sp., Eleusine indica, Diplazium esculentum and Talahib (no known scientific name) were screened using microtiter plate biofilm formation assay for their QS inhibition activity against biofilm formation in Pseudomonas aeruginosa clinical isolate and Pseudomonas aeruginosa PNCM 1335. Extracts of M. micrantha, H. suaveolens flowers, H. vulgaris, A. intermedia, E. indica leaves, D. esculentum and Talahib have inhibitory effect on P. aeruginosa clinical isolate biofilm formation. Decrease in biofilm formation was shown in extracts of S. jamaicensis., M. micrantha, H. suaveolens, H. vulgaris, U. lobata, C. pentandra, A. intermedia, E. indica, D. esculentum and Talahib. against P. aeruginosa PNCM 1335. RNA extracts of M. micrantha, Talahib and A. intermedia exhibited downregulation of lasR in both test bacteria using qRT-PCR analysis through absolute quantification. The prospects of these ethnobotanicals to inhibit bacterial virulence avoiding antibiotic resistance is presented in this paper.
Aggregating algorithms in high dimensional data classification

Field: Computer Science (Physical Sciences)

With the improvements in computer performance and innovations in biological technology, a huge amount of genetic and protein information relevant to diseases can be obtained and recorded rather easily. Analyzing this data however is difficult due to its high dimensionality and the existence of many redundant or noisy features. Many methods have been used, aggregating algorithms have been among the most promising for tackling high dimensional data classification. The most widely used is the Random Forests algorithm. This method is especially attractive because of its prediction accuracy and computational efficiency compared to other tree based methods. Interestingly, despite its wide use, few theoretical studies investigating the factors that may impact the performance of Random Forests, including the number of informative and noisy features, the sample size, and the number of randomly selected features at each node split, have been reported. In this dissertation I take an initial step to analyze the Random Forests algorithm by considering a two-class classification problem where all the features are normally distributed within a class and a stump-tree classifier is used as the base learner. My analysis shows that the random feature selection improves the overall classification accuracy by adaptively assigning voting weights to the weak classifiers according to their performances on the training set. But the adjustment of the weights induced by changing the random selected subset size is very limited. I also claim that bootstrapping original training set enables a larger variety of possible weak classifiers being generated. But the perturbation introduced by bootstrap may deviate from the underlying true distribution of the samples and result in deteriorated weak classifiers. My motivation is to find alternative ways to generate a rich ensemble of weak classifiers that can keep original information and generalize well, and to find a better way to assign weights to the weak classifiers according to their performances and correlations. I proposed the weighted random subspace method. In this method, I addressed the optimal weight assignment problem and proposed solutions under both the independence and dependence assumptions among weak classifiers. Finally, I compared various algorithms on gene expression and protein expression data and confirmed that the weight assignment procedure improves prediction accuracy.
Evaluation ofLATS1andLATS2Promoter Methylation with the Risk of Pterygium Formation

Field: Medicine (Health Sciences)

Purpose . Pterygium is a serious eye problem in countries with high exposure to UV. However, despite numerous studies, the molecular etiology of pterygium is unclear. Recent studies have indicated that LATS1 and LATS2 genes are involved in DDR signaling pathways against continuous UV exposure. Our aim was to evaluate the LATS1 and LATS2 promoter methylation with the risk of pterygium formation. Methods . We evaluated the promoter methylation status of LATS1 and LATS2 using methylation-specific PCR technique. Also, mRNA expression of LATS1 and LATS2 was assessed in 14 cases of pterygium and 14 normal specimens by real-time PCR. Results . Promoter methylation of LATS1 and LATS2 was detected significantly between pterygium tissues and normal tissues [ LATS1 ; OR = 4.9; 95% CI: 1.54 to 15.48,P=0.003; LATS2 ; OR = 7.1; 95% CI: 1.53 to 33.19,P=0.004]. The gene expression analysis showed a statistically significant difference between pterygium tissues and healthy controls for both LATS1 and LATS2 (P<0.05). Conclusions . The data of this study is the first report regarding the effect of promoter methylation of the LATS1 and LATS2 in the pterygium. To confirm these data, doing further studies in various genetic populations with large sample sizes using advanced molecular techniques is proposed.
CHARACTERIZATION OF PHYSICAL ACTIVITIES PERFORMED BY ADOLESCENTS FROM CURITIBA, BRAZIL

Field: Health Professions (Health Sciences)

ABSTRACT Introduction Various studies have been developed and published in relation to the recommendations for physical activity and associated factors. However, there is a lack of studies that detail the places where physical activity is practiced, as well as its frequency, duration and volume. Objective To describe the places, types, frequency, duration and volume of physical activities performed by adolescents in Curitiba, Brazil. Methods A cross-sectional study conducted in 2013-2014, through a household survey with 495 adolescents (12 to 17 years). The places used, and the frequencies of the practice of physical activity were self-reported as either “goes” or “does not go.” The practice of physical activity was determined through the Physical Activity Questionnaire for Adolescents, by type, frequency, duration and weekly volume. The types of physical activity were described with frequency distribution, weekly frequency, duration, and volume, by the median and interquartile range. Gender comparison was tested with the Chi-square and Mann-Whitney U tests (p<0.05). Results The most frequently reported places for physical activity were public squares, parks, soccer fields, schools and sports halls. Soccer fields, schools, sports halls and skate parks were more used by boys, while girls attended gyms (p<0.05). The physical activities most practiced were soccer, skating/rollerblading, cycling, walking and active games. A higher proportion of boys practiced soccer, skating/rollerblading, cycling, running/jogging, and basketball (p<0.05), whereas the physical activities most practiced by girls were walking, walking the dog, dancing, playing games, and gyms (p<0.05). Sports (720 min/week), aerobic exercises (400 min/week) and conditioning exercises (345 min/week) were the activities with the highest weekly volume. Boys showed higher weekly frequency, duration and volume of practice of sports and active games than girls (p<0.05). Conclusion Public places with structures were the most used places, and sports were the most practiced activities. Level of Evidence III; Study of nonconsecutive patients; without consistently applied ‘‘gold’’ reference standard.
The Prostate 70:190 ^199 (2010) Tumor Suppressor PAX6Functions as AndrogenReceptorCo-Repressor to Inhibit

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

BACKGROUND. PAX6, a transcription factor, has currently been suggested to function as a tumor suppressor in glioblastoma and to act as an early differentiation marker for neuroendocrine cells. The androgen receptor (AR) plays a pivotal role in prostate cancer development and progression due to its transcriptional activity in regulating genes involved in cell growth, differentiation, and apoptosis. To determine the role of PAX6 in prostate cancer, we investigated whether PAX6 interacts with AR to affect prostate cancer development. METHODS. We used immunostaining, RT-PCR, and Western blotting assays to show the expression status of PAX6 in prostate tissue and human prostate cancer cell lines. The role of PAX6 in cell growth and colony regeneration potential of LNCaP cells were evaluated byMTT assay and soft agar assay with PAX6-overexpressed LNCaP cells. Mammalian two-hybrid and co-immunoprecipitation (Co-IP) assays were used to demonstrate the interaction between PAX6 andAR. Reporter gene andQ-RT-PCR assays were performed to determine the effects of PAX6 on the function of AR. RESULTS. In prostate cancer tissues, PAX6 expression was stronger in normal epithelial cells than cancer cells, and decreased in LNCaP cells compared to that of DU145 and PC3 cells.
Investigating karst cave sediments of unroofed caves with GPR, XRF and XRD

Field: Earth and Planetary Sciences (Physical Sciences)

Ground penetrating radar (GPR), a nondestructive geophysical method, was used to detect cave sediments, now exposed on the karst surface (in so-called "unroofed caves") due to a general lowering of the surface (dissolution of carbonate rocks). It turned out that cave sediments are expressed as areas with strong signal attenuation on GPR radargrams. In order to test the GPR's capability and reliability in detecting cave sediments, further mineralogical-geochemical analyses were conducted to reveal which factors influence the attenuation the most. At the testing location, samples of cave sediments and soils on carbonate rocks were taken for X-ray diffraction (XRD) and X-ray fluorescence (XRF) analyses to compare the mineral and geochemical compositions of both sediments. Results show that cave sediments contain higher amounts of clay minerals and iron/aluminum oxides/hydroxides which can strongly affect GPR penetration. Differences in the mineral composition also lead to water retention in cave sediments even through dry periods which additionally contribute to increased attenuation with respect to surrounding soils. Based on these findings, GPR profiling was used on several other places where direct indicators of unroofed caves are not present due to strong surface reshaping. GPR has proven to be a reliable method for locating these areas and can be a valuable complementary method to geological mapping for a more comprehensive recognition of unroofed cave systems. These are important for understanding karst erosion processes and geomorphology. For instance, studying unroofed cave systems can help with reconstructing the direction of former underground water flows.
Histo- and cytochemistry of acetylcholinesterase activity at the myotendinous junction in skeletal muscles of rats.

Field: Neuroscience (Life Sciences)

The acetylcholinesterase (AChE) activity at the myotendinous junction (MTJ) in several skeletal muscles of limbs and trunks of adult rats and in M. soleus and M. gastrocnemius of newborn rats with or without denervation of sciatic nerves was studied under a light microscope and an electron microscope. Under an electron microscope the AChE activity at the MTJ was detected in the lamina rara. In M, soleus and M. rectus abdominis of adult rats nearly all fibers exhibited AChE activity and in other muscles of adult rats a few fibers exhibited the activity. In M. gastrocnemius of newborn rats the percentage of AChE-positive MTJ was higher than that of adult rats. As they grew the activity gradually decreased. There were AChE-positive and AChE-negative MTJs in muscle. The Z lines of the muscle fiber, which had AChE-positive MTJ, were wider than those of the fiber, which had AChE-negative MTJ. In the denervated muscles, the AChE activity at the MTJ was detected three weeks after the denervation in adult rats and one month after the denervation in newborn rats. In the atrophic muscles the AChE activity could not be detected under a light microscope, but was detected slightly under an electron microscope. The present results suggest that AChE activity is detected at the MTJ in the red muscle fiber and the enzyme seemed to be myogenic.
An Encoder-Decoder Based Approach for Anomaly Detection with Application in Additive Manufacturing

Field: Computer Science (Physical Sciences)

We present a novel unsupervised deep learning approach that utilizes an encoder-decoder architecture for detecting anomalies in sequential sensor data collected during industrial manufacturing. Our approach is designed to not only detect whether there exists an anomaly at a given time step, but also to predict what will happen next in the (sequential) process. We demonstrate our approach on a dataset collected from a real-world Additive Manufacturing (AM) testbed. The dataset contains infrared (IR) images collected under both normal conditions and synthetic anomalies. We show that our encoder-decoder model is able to identify the injected anomalies in a modern AM manufacturing process in an unsupervised fashion. In addition, our approach also gives hints about the temperature non-uniformity of the testbed during manufacturing, which was not previously known prior to the experiment.
Cytological Aspects of Cervico-Uterine Smears from HIV/HPV HR Coinfected Women Treated with Antiretrovirals

Field: Medicine (Health Sciences)

Introduction: Women living with HIV are at high risk of developing persistent HPV-HR infections. This favors the development of precancerous lesions that may progress to cervical cancer. With a view to improving management and taking preventive action against cervical lesions and cervical cancer in women living with HIV, our study aimed to describe cervical abnormalities and establish a relationship between lesion severity and HPV-HR genotypes in HIV/HPV-HR co-infected women. Methodology: This was a descriptive cross-sectional study conducted at the CTAB from March 2021-December 2022. Of 122 women living with HIV screened HPV HR positive 90 presented for FCU. Cervico-uterine smears were read after Papanicolaou staining by two cytopathologists at the anatomy-cytology-pathology laboratory of the university hospital center. Results were rendered according to the 2014 Bethesda system classification, and data processing was performed using SPSS 25 software. Results: 90 patients co-infected with HIV/HPV-HR were included, with a mean age of 44.16±10.08 years, ranging from 20 to 70 years. The women in our study were all on triple therapy, and most had a controlled viral load and CD4 count above 200mm3. Cytological abnormalities accounted for 38.9%, with a predominance of atypical squamous cells of undetermined significance (ASCUS) 51.43%, followed by low-grade squamous intraepithelial lesions (LSIL) 37.14% and 11.43% of atypical squamous cells for which a high-grade lesion could not be excluded (ASC-H). Triple therapy had a protective impact in women against progression to precancerous states, although no statistically significant association was observed between cervical lesions and HR-HPV genotypes (p=0.819). Conclusion: Our study reveals a high proportion of ASCUS lesions in women living with HIV and co-infected with HPV HR. Triple therapy has a protective effect against progression to severe lesions. To this end, screening for precancerous lesions in this population should include diagnosis of the P16 protein by Histoimmuno chemistry. Key words: FCU, HR- HPV, Women, HIV, ARV, Congo.
The Challenges and Opportunities in Training Muslim Chaplaincy Students for a Burgeoning New Field

Field: Social Sciences (Social Sciences)

Though a relatively new field, Islamic chaplaincy has become integral to many spiritual care and religious life divisions of public institutions that have undergone a significant shift towards a multifaith presence in approximately the last fifty years. These changes promote new opportunities in which Muslim chaplains can enrich religious life through their distinctive contributions to the field. Simultaneously, there are challenges that need to be addressed such as hiring practices that provide balanced support for Muslim chaplains, the avoidance of tokenization tendencies through ensuring the proper education of students training to become Muslim chaplains, and the need for such students to have their own space for development and formation that does not compromise their religious identities in Christian majority contexts. These challenges have facilitated creative solutions as well as calls for action from interfaith allies.
Effects of Magnetic Fields Generated by Different Permanent Magnet Arrays on Image Reconstruction in a Low-Field Portable MRI System

Field: Engineering (Physical Sciences)

A portable magnetic resonance imaging (MRI) imager may help this medical imaging modality to reach out areas that are remote or/and hard to access, and situations that the environment is dynamic, for example, in an ambulance. Permanent magnet array is a popular option to supply the main magnetic field for imaging. It allows portability, does not consume power, and guarantees a low cost. However, the magnet field it generates does not have a linear gradient, thus the acquired signals from the system and the image are not directly linked by Fourier Transformation. There are different kind of magnet arrays that can be used in a portable system. Halbach array with a transverse magnetic field provide an option. Besides, Aubert array with a longitudinal magnetic field that was recently proposed is a good alternative [1]-[2]. For a magnet array, the field strength, field homogeneity, and field pattern are directly related to the quality of image reconstruction [3]. In this talk, different magnet arrays and the characteristics of the magnetic fields they generate for imaging in a low-field MRI system will be introduced. The effects of the magnetic fields on the image reconstruction will be analysed in detail.
Microbial synthesis of Bio-polymers of Polyhydroxybutyrate (PHB) from spent wash as low-cost carbon source in the medium

Field: Immunology and Microbiology (Life Sciences)

The use of plastics is widespread, from the automotive to the medical industries. The plastic takes a very long time to break down and is bad for the environment. It is best to use biodegradable plastics rather than such non-biodegradable polymers. The biopolymer polyhydroxybutyrate (PHB) has characteristics similar to those of synthetic polymers and is vulnerable to microbial deterioration in the environment. Microorganisms like yeast and bacteria produce PHB when under stress. The primary objective of the study was to isolate bacterial strains from soil capable of generating PHB. Sudan Black B was used to detect PHB for the initial screening of the isolates. The method of digestion with sodium hypochlorite was used to extract PHB. PHBs that had been extracted were measured using UV-VIS spectroscopy and identified using FTIR and DSC.
Methotrexate treatment suppresses osteoblastic differentiation by inducing Notch2 signaling and blockade of Notch2 rescues osteogenesis by preserving Wnt/β‐catenin signaling

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Abstract Methotrexate (MTX) is a commonly used antimetabolite in cancer treatment. Its intensive use is linked with skeletal adverse effects such as reduced bone formation and bone loss, and yet little information is available on molecular mechanisms underlying MTX‐induced impaired bone formation. This study investigated the effects of MTX treatment at a clinical chemotherapy relevant dose on osteogenic differentiation in MC3T3E1 osteoblastic cells. To investigate the potential mechanisms, the expression of 87 genes regulating osteoblast differentiation and bone homeostasis was screened in MTX‐treated versus untreated cells by polymerase chain reaction (PCR) arrays and results illustrated significant upregulation of Notch2 and Notch target genes at both early and late stages of MC3T3E1 differentiation following MTX treatment. To confirm the roles of Notch2 pathway and its potential action mechanisms, MC3T3E1 cells were treated with MTX with an anti‐Notch2 neutralizing antibody or control IgG and effects were examined on osteogenesis and activation of the Wnt/ β ‐catenin pathway. Our results demonstrated that induction of Notch2 activity is associated with MTX adverse effects on osteogenic differentiation and blocking Notch2 rescues osteoblast differentiation by preserving activation of the Wnt/ β ‐catenin pathway.
Nafcillin Continuous Infusion Versus Intermittent Infusion Therapy in Pediatric Patients

Field: Medicine (Health Sciences)

Background: Beta-lactam antibacterials exhibit time-dependent killing, meaning that efficacy is associated with the percentage of time that serum drug concentrations exceed the minimum inhibitory concentration (MIC) at the infection site.Nafcillin is an anti-staphylococcal penicillin commonly used in the treatment of infections caused byStaphylococcus aureus.It is traditionally dosed intermittently (every 4 to 6 hours),but continuous infusions allow persistent drug concentrations while decreasing nursing time and IV catheter manipulations. Safety and efficacy of continuous and intermittent infusions of nafcillin have not been compared.Theprimary objective of this study is to compare the efficacy and safety of a continuous nafcillin dosing regimen with that of an intermittent dosing regimen.\nMethods: A retrospective cohort study of patients who received nafcillin at Riley Hospital for Children from January 1, 2009 to December 31st, 2012 was completed. Patients at least 30 days old who received more than one dose of nafcillin dosed intermittently (every 4 or 6 hours) or continuously were included. Electronic medical records were reviewed to determine the primary outcome of efficacy. Time to normalization of white blood cell count, immature neutrophil count, body temperature, and inflammatory markers as well as resolution of symptoms specific to the site of infection, as described by the treating physician, were included in the analysis. Presence of adverse drug reactions and factors that may have confounded efficacy or safety outcomes were also collected.\nResults:Data analysis is ongoing. Results and conclusion will be presented at the 2014 Butler University Undergraduate Research Conference.