jimnoneill/paper-to-field-training huggingface dataset:
Characterization of Boolean Networks with Single or Bistable States

Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since understanding bistability is key for understanding these biological systems, mathematical modeling of the bistability phenomenon has been at the focus of researches in quantitative and system biology. Recent study shows that Boolean networks offer relative simple mathematical models that are capable of capturing these essential information. Thus a better understanding of the Boolean networks with bistability property is desirable for both theoretical and application purposes. In this paper, we describe an algebraic condition for the number of stable states (fixed points) of a Boolean network based on its polynomial representation, and derive algorithms for a Boolean network to have a single stable state or two stable states. As an example, we also construct a Boolean network with exactly two stable states for the lac operon's $β$-galactosidase regulatory pathway when glucose is absent based on a delay differential equation model

Topic: Gene Regulatory Network Analysis
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
On self-directed learning

Article Free Access Share on On self-directed learning Authors: Shai Ben-David Computer Science Department, Technion, Haifa 32000, Israel Computer Science Department, Technion, Haifa 32000, IsraelView Profile , Nadav Eiron Computer Science Department, Technion, Haifa 32000, Israel Computer Science Department, Technion, Haifa 32000, IsraelView Profile , Eyal Kushilevitz Computer Science Department, Technion, Haifa 32000, Israel Computer Science Department, Technion, Haifa 32000, IsraelView Profile Authors Info & Claims COLT '95: Proceedings of the eighth annual conference on Computational learning theoryJuly 1995 Pages 136–143https://doi.org/10.1145/225298.225314Online:05 July 1995Publication History 2citation339DownloadsMetricsTotal Citations2Total Downloads339Last 12 Months11Last 6 weeks5 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

Topic: Machine Learning and Algorithms
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Tropical Geometric Variation of Tree Shapes

Abstract We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is given by the tree’s branching configuration and leaf labeling. We use the tropical line segment as a framework to define notions of variance as well as invariance of tree topologies: we provide a combinatorial search theorem that describes all tree topologies occurring along a tropical line segment, as well as a setting under which tree topologies do not change along a tropical line segment. Our study is motivated by comparison to the moduli space endowed with a geodesic metric proposed by Billera, Holmes, and Vogtmann (referred to as BHV space); we consider the tropical geometric setting as an alternative framework to BHV space for sets of phylogenetic trees. We give an algorithm to compute tropical line segments which is lower in computational complexity than the fastest method currently available for BHV geodesics and show that its trajectory behaves more subtly: while the BHV geodesic traverses the origin for vastly different tree topologies, the tropical line segment bypasses it.

Topic: Chemical synthesis and alkaloids
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Flight test measurements and analysis of sonic boom phenomena near the shock wave extremity

The sonic boom flight test program conducted at Jackass Flats, Nevada, during the summer and fall of 1970 consisted of 121 sonic-boom-generating flights over the 1500 ft instrumented BREN tower. This test program was designed to provide information on several aspects of sonic boom, including caustics produced by longitudinal accelerations, caustics produced by steady flight near the threshold Mach number, sonic boom characteristics near lateral cutoff, and the vertical extent of shock waves attached to near-sonic airplanes. The measured test data, except for the near-sonic flight data, were analyzed in detail to determine sonic boom characteristics for these flight conditions and to determine the accuracy and the range of validity of linear sonic boom theory. The caustic phenomena observed during the threshold Mach number flights and during the transonic acceleration flights are documented and analyzed in detail. The theory of geometric acoustics is shown to be capable of predicting shock wave-ground intersections, and current methods for calculating sonic boom pressure signature away from caustics are shown to be reasonably accurate.

Topic: Aerodynamics and Acoustics in Jet Flows
Subfield: Aerospace Engineering
Field: Engineering
Domain: Physical Sciences
Supplementary Table 3 from Gene Expression Profiling using Nanostring Digital RNA Counting to Identify Potential Target Antigens for Melanoma Immunotherapy

&lt;p&gt;XLSX file - 93K, Supplemental Table S3. TUMORS: 1 2 3 4 5 6 MELANOMA RELATED GENES.&lt;/p&gt;

Topic: RNA Interference and Gene Delivery
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
The Effect Of Debt Covenant, Tunneling Incentive, Bonus Mechanism And Firm Size On Transfer Pricing

The purpose of this study was to determine the effect of Debt Covenant, Tunneling Incentive, Bonus Mechanism and Firm Size on Transfer Pricing in manufacturing companies listed on the Indonesia Stock Exchange (IDX). The research time period used is 5 years, namely the 2019-2023 period. The population of this study includes all manufacturing sector companies listed on the Indonesia Stock Exchange (IDX) for the 2019-2023 period. The sampling technique used purposive sampling technique. Based on the predetermined criteria, 28 companies were obtained. The type of data used is secondary data obtained from the Indonesia Stock Exchange website. The analysis method used is panel data regression analysis. This research uses Eviews 12.0. The result shows that: (1) Debt Covenant affects transfer pricing, (2) Tunneling Incentive affects transfer pricing, (3) Bonus Mechanism has no effect on transfer pricing, (4) Firm Size has no effect on transfer pricing.

Topic: Financial Analysis and Corporate Governance
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
Multi-Robot Indoor Environment Map Building Based on Multi-Stage Optimization Method

For a multi-robot system, the accurate global map building based on a local map obtained by a single robot is an essential issue. The map building process is always divided into three stages: single-robot map acquisition, multi-robot map transmission, and multi-robot map merging. Based on the different stages of map building, this paper proposes a multi-stage optimization (MSO) method to improve the accuracy of the global map. In the map acquisition stage, we windowed the map based on the position of the robot to obtain the local map. Furthermore, we adopted the extended Kalman filter (EKF) to improve the positioning accuracy, thereby enhancing the accuracy of the map acquisition by the single robot. In the map transmission stage, considering the robustness of the multi-robot system in the real environment, we designed a dynamic self-organized communication topology (DSCT) based on the master and slave sketch to ensure the efficiency and accuracy of map transferring. In the map merging stage, multi-layer information filtering (MLIF) was investigated to increase the accuracy of the global map. We performed simulation experiments on the Gazebo platform and compared the result of the proposed method with that of classic map building methods. In addition, the practicability of this method has been verified on the Turtlebot3 burger robot. Experimental results proved that the MSO method improves the accuracy of the global map built by the multi-robot system.

Topic: Robotics and Sensor-Based Localization
Subfield: Aerospace Engineering
Field: Engineering
Domain: Physical Sciences
Prolongation of the Q-T Interval in a Victim of Sudden Infant Death Syndrome

A 3-week-old infant died of sudden infant death syndrome (crib death, cot death). Although prolongation of the Q-T interval was found on an electrocardiogram taken at birth, this child appeared to have died of terminal respiratory failure as judged by a postmortem arterial oxygen tension of 4 mm Hg. The heart showed right ventricular hypertrophy, a finding consistent with chronic hypoxemia. The prolongation of the Q-T interval may have contributed to the death of this child with hypoxia predisposing to a fatal episode of ventricular fibrillation.

Topic: Neuroscience of respiration and sleep
Subfield: Endocrine and Autonomic Systems
Field: Neuroscience
Domain: Life Sciences
Teaching Digital Humanities Tools at a Distance: A Librarian-Instructor Partnership Integrating Scalar into a Graduate Distance Course

This paper presents the process and outcomes of a digital humanities (DH) teaching collaboration. The authors, a subject librarian and an instructor for a distance graduate course on the history of children’s literature, will discuss features of the collaboration and course design: the digital literacy learning outcomes, the authors’ choice of the multi-media publishing platform Scalar as the best fit for those outcomes, and their design of the assignment sequence to achieve learning outcomes and assess student learning.

Topic: Digital Humanities and Scholarship
Subfield: Literature and Literary Theory
Field: Arts and Humanities
Domain: Social Sciences
The adaptive nature of protein residue networks

Protein residue networks PRNs are used to describe proteins. These networks are usually based on an average structure for the protein. However, proteins are dynamic entities that are affected by their surroundings. In this work, we study the effect of temperatures above and below the protein dynamical transition temperature(≈200 K), on three important network parameters gleaned from weighted PRNs for the solvated β-lactamase inhibitory protein BLIP: the betweenness centrality B, the closeness centrality C, and the clustering coefficient CC. The B and C values will be extracted for each node from PRNs at six different temperatures: 150 K, 180 K, 200 K, 220 K, 250 K, and 310 K respectively. The average value for the CC for each PRN will also be calculated at each temperature, respectively. We find that at temperatures ≤200 K, the network nodes with the most significant B and C values tend to have lower relative solvent accessibility RSA values, and to fall within the protein secondary structure elements (α helices and β sheets). At temperatures >200 K, the significant nodes in terms of B and C tend to have larger RSA values, and to fall on the connecting loops in the protein. The average CC decreases in value for the PRNs up to 200 K, and then remains basically constant above 200 K. This clearly shows that any conclusions based on static PRNs should be handled with care. The dynamic nature of proteins and its coupling to the surrounding environment should be taken into consideration when using the PRN paradigm. Proteins 2017; 85:917-923. © 2016 Wiley Periodicals, Inc.

Topic: Protein Structure and Dynamics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Luteolin Inhibits the Activity, Secretion and Gene Expression of MMP-3 in Cultured Articular Chondrocytes and Production of MMP-3 in the Rat Knee

We investigated whether luteolin affects the gene expression, secretion and activity of matrix metalloproteinase-3 (MMP-3) in primary cultured rabbit articular chondrocytes, as well as production of MMP-3 in the rat knee to evaluate the potential chondro-protective effects of luteolin. Rabbit articular chondrocytes were cultured in a monolayer and IL-1β-induced gene expression levels of MMP-3, MMP-1, MMP-13, a disintegrin and metalloproteinase with thrombospondin motifs-4 (ADAMTS-4), ADAMTS-5 and type II collagen were measured by reverse transcription - polymerase chain reaction (RT-PCR). Effects of luteolin on interleukin-1β (IL-1β)-induced secretion and enzyme activity of MMP-3 in rabbit articular chondrocytes were investigated by western blot analysis and casein zymography, respectively. The effect of luteolin on MMP-3 protein production was also examined in vivo. The results were as follows: (1) luteolin inhibited the gene expression levels of MMP-3, MMP-1, MMP-13, ADAMTS-4 and ADAMTS-5. However, it increased the gene expression level of collagen in rabbit articular chondrocytes; (2) luteolin inhibited the secretion and activity of MMP-3; (3) luteolin inhibited in vivo production of MMP-3 protein. These results suggest that luteolin can regulate the gene expression, secretion and activity of MMP-3, by directly acting on articular chondrocytes.

Topic: Protease and Inhibitor Mechanisms
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
[Hospitalizations due to falls in the childhood population of northern Israel: a comparison between the years 1993-1995 and 2002-2004].

Previous studies showed that falls from height are a major cause of morbidity in children who live in northern Israel. These studies demonstrated major differences in injury severity between Arab and Jewish children, and noted that more children from the Arab sector were admitted to the Intensive Care Unit (ICU). The objective of this study was to compare the hospitalization rates at Rambam Medical Center in the years 1993-1995 and 2002-2004, and to evaluate selected demographic characteristics of these hospitalizations. We found that the total number of falls increased significantly during the years 2002-2004, and that a dramatic increase in the number of admission to ICU was notable among the Jewish population. These findings suggest that injury prevention programs should be implemented urgently on a national level.

Topic: Injury Epidemiology and Prevention
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Going back and beyond: children’s learning through places

In 1919, the Canadian province of British Columbia (BC) established the Elementary Correspondence (EC) School to provide formal education for children living in rural areas with difficult access to a school. Through children's letters, this paper interrogates the concept of place, a key one for placed-based approaches to environmental education. Place-based education has focused on natural and rural environments to engage students in environmental learning, sometimes presenting the desirability of connectedness to nature and the local community with nostalgia and romanticism. Children's letters suggest that their learning has long been shaped by their places, material and imaginary, and that the EC school was a place as important as nature in children's learning and schooling. Children's letters contribute a rich historical perspective that helps to rethink the rural/urban divide into a relationship of mutual constitution of childhood and nature across time and space.

Topic: Indigenous and Place-Based Education
Subfield: Education
Field: Social Sciences
Domain: Social Sciences
Skeletal Benefits of Pre-Menarcheal Gymnastics Are Retained After Activity Cessation

Mechanical loading during childhood and adolescence may yield skeletal benefits that persist beyond activity cessation and menarche. At 1 year pre- and 2 years post-menarche, nondominant forearm areal bone mineral density (aBMD), bone mineral content (BMC) and projected area (area) were compared in gymnasts ( n = 9), ex-gymnasts ( n = 8) and nongymnasts ( n = 13). At both observations, gymnasts and ex-gymnasts had higher forearm aBMD, BMC and area than nongymnasts. gymnasts had higher postmenarcheal means than ex-gymnasts for all three parameters. Childhood mechanical loading yields skeletal advantages that persist at least 24 months after loading cessation and menarche. Continued postmenarcheal loading yields additional benefit.

Topic: Body Composition Measurement Techniques
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
[Moschcowitz's disease--effect of therapeutic plasma exchange and splenectomy].

Moszkowicz's disease (thrombotic thrombocytopenic purpura), TTP, is an uncommon haematologic, neurologic syndrome which, almost regularly, terminates fatally. The disorder has a turbulent and fulminant course and is of short duration. The presented patient was treated with a combined therapeutic modality of intensive plasma exchange and subsequent splenectomy. This is the first case of successful treatment of TTP in Yugoslavia. The previous therapeutic approaches with infusions of fresh frozen plasma produced only transient or dubious responses. Clinical remissions were rare. In this patient, however, the plasma exchange with volume adjustment with the fresh frozen plasma or albumin produced restitution of the thrombocyte count to normal values and disappearance of all neurological signs and complaints. At that point surgical splenectomy was carried out with the concomitant extirpation of an accessory spleen circumstantially detected on exploration. Pathohistology of both spleens revealed typical tissue changes (disseminated hyaline and thrombocyte thrombi of small blood vessels) characteristic of Moszkowicz's disease. Following an uneventful splenectomy and discontinuation of all medicamentouse therapy the normal thrombocyte count was maintained without no sign of recurrence of neurological symptoms or manifestations.

Topic: Complement system in diseases
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
An integrated approach with vardenafil orodispersible tablet and cognitive behavioral sex therapy for treatment of erectile dysfunction: a randomized controlled pilot study

Erectile Dysfunction is considered a multifactorial disease, where organic and psychological aspects are often interconnected. In a randomized controlled pilot study, we compared the efficacy of combined vardenafil orodispersible tablet (VARD) and cognitive-behavioral sex therapy (CBST) vs. VARD alone in improving sexual symptoms in both male and female partners. Thirty male patients with erectile dysfunction, and their partners were randomly assigned with a 2 : 1 ratio, to two different arms and treated for 10 weeks with VARD (Group A; n = 19) or VARD+CBST (Group B; n = 11). International Index of Erectile Dysfunction (IIEF-15), Female Sexual Function Index (FSFI) and Index of Sexual Satisfaction (ISS) were, respectively, administered to male, female, and both partners at times (T) 0, 1 (+5 weeks of therapy) and 2 (+10 weeks of therapy). Groups A and B were similar in their sociodemographic and clinical characteristics. Pre-treatment (T0) test scores did not significantly differ among the groups. In both group A and B, the IIEF-Erectile Function domain showed a significant improvement from T0 to T1 (p = 0.005 and p < 0.0001 vs. T0, respectively) and from T0 to T2 only in group B (p = 0.013). In group A, FSFI and both male and female ISS did not show any significant change at T1 and T2 vs. T0. In group B, a significant improvement at final time-point in FSFI and male and female ISS scores was reported (p < 0.05, T2 vs. T0 in all scores). The results of our study suggest that both VARD alone and VARD+CBST improved erectile function, however, only VARD+CBST improved couple sexual satisfaction and female sexual function.

Topic: Sexual function and dysfunction studies
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Cracks in the Evidence: Why Studies from COURAGE to ISCHEMIA Failed to Show Benefit of Stenting PCI

Percutaneous Coronary Intervention (PCI) with stenting remains widely utilized for managing Chronic Coronary Syndrome (CCS). However, landmark clinical trials such as COURAGE and ISCHEMIA have repeatedly shown no significant advantage of PCI with stenting over Optimal Medical Therapy (OMT). This review critically analyses methodological limitations, including overlooked Vulnerable Plaques (VPs), Incomplete Revascularization (IR), inherent procedural risks, long-term stent complications, and the consistent lack of mortality benefits. Furthermore, unique challenges in translating these international trial results into the Indonesian healthcare context, such as medication adherence issues, quality disparities in interventional practice, and distinct medico-legal pressures, are discussed. Bethsaida Hospital in Indonesia, led by Prof. Dasaad Mulijono, has successfully addressed these limitations through a pioneering integrated approach combining PCI utilizing Drug-Coated Balloon (DCB) technology, rigorous OMT, and a Whole-Food Plant-Based Diet (WFPBD), resulting in exceptional outcomes, including markedly reduced rates of target lesion revascularization (2%), virtually no myocardial infarctions or PCI-related mortalities, and effective management of VPs. Recognizing these limitations and contextual factors is crucial for informed, individualized CCS treatment decisions. If leading Indonesian cardiology centres can replicate and sustain these strategies, stenting PCI in CCS may be justified.

Topic: Coronary Interventions and Diagnostics
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
ARMC10 Drives Glioblastoma Progression Through Activating Notch Pathway

ABSTRACT This study aimed to check the biological functions and uncover the mechanism of armadillo repeat protein C10 (ARMC10) in glioblastoma (GBM). The expression and potential mechanisms of ARMC10 in GBM were analyzed by bioinformatics analysis. In GBM cells, function‐loss experiments were used to evaluate the influences of ARMC10 on cell proliferation, cell invasion, lipid levels, and cell migration by colony formation assay, 5‐ethynyl‐2′‐deoxyuridine staining, cell counting kit‐8 assay, transwell assay, BODIPY staining, and wound healing assay. Mouse xenograft models were constructed to validate the influences of ARMC10 in vivo. ARMC10 levels in GBM were upregulated, and patients with low ARMC10 levels displayed a better prognosis. ARMC10 knockdown resulted in a decrease of GBM cell invasion, migration, and proliferation. GSEA showed that ARMC10 was positively associated with the Notch pathway and fatty acid metabolism. ARMC10 knockdown reduced the levels of triglyceride, cholesterol, and lipid, and inhibited the expression of proteins related to fatty acid metabolism and Notch pathway. Moreover, notch receptor 1 (Notch1) overexpression reversed the inhibition of cell proliferation, fatty acid metabolism, and invasion induced by ARMC10 knockdown. In vivo, ARMC10 knockdown suppressed tumor growth. RMC10 knockdown suppressed GBM malignant progression, which had a bearing on Notch pathway.

Topic: MicroRNA in disease regulation
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences