jimnoneill/paper-to-field-training huggingface dataset:
Notch Signaling in Tumor Angiogenesis

Field: Medicine (Health Sciences)

Notch signaling plays an important role in developmental and pathological angiogenesis. Notch ligands, Dll4 and Jag1, have been implicated in tumor angiogenesis. Inhibition of Dll4-mediated Notch signaling results in hypersprouting of non-functional vasculature in tumors. We have constructed and analyzed pan-Notch ligand inhibitors, Notch1 decoys 1-24 and 1-36, which are based on the extracellular EGF-like repeats of Notch1. Both Notch1 decoys block angiogenesis in in vitro endothelial cell-based assays and in the mouse retina. We also show that they similarly inhibit Dll4- and Jag1-induced Notch signaling in vitro and result in a significant decrease in tumor growth and tumor vasculature in mouse and human tumor xenograft models. Interestingly, truncated Notch1 decoy variants, Notch1 decoys 1-13 and 10-24, act as ligand-specific Notch inhibitors. Notch1 decoy 1-13 is Dll4-specific whereas Notch1 decoy 10-24 is Jag1-specific. Ligand-specific Notch1 decoys effectively reduce tumor growth in tumor xenograft models in the mouse, including Mm5MT-FGF4, KP1-VEGF, LLC, and B16-F10. Notch1 decoy 1-13 has been demonstrated to increase tumor vasculature by increasing endothelial sprouting and number of tip cells. However, similar to the previously reported effects of Dll4 blockade, the tumor vessels are poorly perfused and hardly functional. On the other hand, Jag1-specific Notch1 decoy 10-24 significantly reduces tumor vessel density and disrupting endothelial-pericyte interactions, causing the impaired vascular structure and attenuated vascular perfusion. In addition, Notch1 decoys 1-13, 10-24, and 1-24 show an anti-metastatic potential in causing a delay of lung metastasis in the B16-F10 tumor model. Unlike gamma-secretase inhibitors and Dll4-blocking agents, Notch1 decoys do not cause GI-associated toxicity or vascular neoplasms. Therefore, our Notch1 decoys may represent a novel alternative and may hold future promise for Notch-targeted cancer therapy.
Ureteroscopy clinical applications in urology

Field: Medicine (Health Sciences)

Objective:To investigate the ureteroscopy in the diagnosis and treatment of urological clinical value.Methods:From March 2004 to January 2010 ureteroscopic diagnosis and treatment techniques were 416 cases of urinary system diseases, including 387 cases of ureteroscopic therapy, used in diagnosis of 29 patients (side).Results:Ureteral calculi stones in the lower success rate was 96.8%(176/182), ureteral stone stone success rate was 69.6%(56/81).The diagnosis and treatment of urinary tract diseases in children under the application of ureteroscopy satisfactory effect.Lower urinary tract stones in adults, especially in patients with urethral stricture ureteroscopy good effect.19 patients for the diagnosis of minimally invasive way to clear the diagnosis.Operation failed in 4 cases, serious complications occurred in 12 cases.Conclu-sion:The wide clinical application in urology ureteroscopy for lower ureteral stones in the preferred ureteroscope, minimally invasive treatment for pediatric urology has unique advantages in other common urological diseases, application of minimally invasive diagnosis and treatment of choice.
Periostin as a marker of eosinophilic inflammation in patients with asthma and chronic obstructive pulmonary disease

Field: Medicine (Health Sciences)

BACKGROUND: Asthma and chronic obstructive pulmonary disease are common chronic respiratory diseases. Given their heterogeneity, the study of periostin is a relevant area for establishing the endotypes of airway inflammation and determining further therapy tactics. AIM: To evaluate periostin levels and determine its significance as a marker of eosinophilic inflammation in patients with asthma and chronic obstructive pulmonary disease. MATERIALS AND METHODS: The study included 59 patients with asthma and 33 patients with chronic obstructive pulmonary disease. The control group consisted of 37 apparently healthy people, comparable in age and sex, without allergic and bronchial obstructive diseases in anamnesis. The anamnesis data, the number of peripheral blood eosinophils and induced sputum, indices of external respiratory function were evaluated. Levels of specific immunoglobulin E to allergens, periostin level were determined in blood serum by immunoenzyme method. The obtained data were processed using STATISTICA 13 and SPSS Statistic 27 software systems. RESULTS: The maximum serum periostin concentration 22.5 (17–38) ng/ml was recorded in the patients with asthma, which was significantly higher than in the chronic obstructive pulmonary disease group [16 (12–21) ng/ml; p = 0.006] and control group [20.1 (14.6–24.8) ng/ml; p = 0.044]. The level of periostin in induced sputum in the patients with asthma was significantly higher than in the chronic obstructive pulmonary disease group — 0.05 (0.03–0.6) ng/ml vs 0.03 (0.02–0.04) ng/ml (p = 0.008). The study revealed the correlation between serum periostin level and eosinophil level (r = 0.406; p 0.05) and with forced expiratory volume in the first second after bronchodilator test (r = 0.366; p 0.05) as well as with forced expiratory volume in the first second divided by forced vital capacity after bronchodilator test (r = 0.572; p 0.05). CONCLUSIONS: Periostin is a promising marker of eosinophilic inflammation in patients with asthma, which can be considered as an indicator of fixed bronchial obstruction and a molecule linking T2-inflammation and airway remodelling. In a group of chronic obstructive pulmonary disease patients, the use of periostin for diagnostic and prognostic purposes requires further investigation and larger studies.
Apoptosis rate in human spermatozoa: a sperm quality assay.

Field: Medicine (Health Sciences)

Several studies have demonstrated the relationship between gonadotrophine serum levels and the apoptosis rate in germinal cells (Bosco et al 2005). In human, lower FSH serum levels are associated with reduced Sperm Standard Parameters in term of concentration, motility and morphology and higher sperm DNA fragmentation. Hypogonadotrope hypogonadism is a clinical condition associated with male infertility, characterized by low serum levels of gonadotrophins. \nIn this pilot study we investigated the spermatozoa quality of 11 patients with development of hypogonadotrope hypogonadism urdergoing in vitro fertilization programs. Recombinant-FSH administered to improve the sperm parameters, apoptosis rate, aiming to increase the success of in vitro fertilization techniques. We found an effective procedure to highlight the correlation between spermatozoa morphology and DNA fragmentation, by TUNEL assay in situ. Spermatozoa integrity DNA influences reproductive potentiality and increases IVF outcome.
Micro‐Counseling: An Experimental Study of Pre‐Practicum Training in Communicating Test Results

Field: Psychology (Social Sciences)

Micro‐counseling techniques were used to train 10 beginning graduate students in communicating test results. Training emphasized listening and responding to cues given by the client, brief and concise statements about test‐related information, and relating the information to the client's experiences and needs. Training aids included programmed materials, brief videotapes of positive and negative models, role‐playing, and videotape feedback of the role‐playing and test interpretation sessions. Judges' ratings of trainees in the experimental group were significantly higher than their ratings for the 10 trainees in the control group. Client ratings of counselor effectiveness did not differ significantly for the two groups. Changes in clients' pre‐ and post‐test attitude scores and knowledge scores were statistically significant. An enthusiastic response to the micro‐counseling approach was evident from both inexperienced and experienced graduate students.
242 Monitoring MDSC – a hurdle to immune checkpoints inhibitors

Field: Medicine (Health Sciences)

Background

Certain cell subsets have been identified to have a negative impact on cancer immunotherapies by promoting angiogenesis and immunosuppression in the tumor microenvironment. One of these cell subsets is a heterogeneous population of immature myeloid cells that have been named Myeloid Derived Suppressor Cells (MDSC). MDSC are increased in states of cancer and their numbers have been shown to inversely correlate with a positive clinical outcome. These findings have prompted the measurement of MDSC in order to predict clinical outcome during treatment with immunotherapies. In this study, flow cytometry was used to measure M-MDSC in frozen PBMC samples and hence predict medical outcome in melanoma patients treated with an anti-CTLA-4 drug (ipilimumab).

Methods

M-MDSC were measured in frozen PBMC from 20 healthy donors and 68 patients with melanoma treated with ipilimumab. M-MDSC were enumerated using a Lin-CD14+CD11b+HLA-DRlow/- phenotype. In order to prevent subjectivity during gating, caused by the lack of bi-modality with HLA-DR staining, a computational algorithm was used. As distinct HLA-DR spread can be observed in the different subjects, measuring the CV (a ratio between GMFI and SD) of this spread allows to calculate a standardized ad hoc quantitative measure of MDSC frequency in cancer patients. This measurement enables identification of M-MDSC in an objective manner and was used to determine whether the percentage of M-MDSC in patients could be linked with overall survival.

Results

The relative frequency of M-MDSC was determined in 68 melanoma patients treated with two different doses of ipilimumab. By comparing the percentage of M-MDSC at baseline (pre-treatment) and after two doses of ipilimumab with the overall survival data and applying log-rank statistics, a cut-off was defined allowing the separation of 'high' and 'low' M-MDSC expressers. Patients with 'low' M-MDSC were associated with improved overall survival with a hazard ratio of 0.35.

Conclusions

The reliable measurement of immune suppressive cells such as MDSC gives the ability to predict the clinical outcome of cancer treatments. In turn, these measurements will permit the design of patient-specific treatments as inhibitors to these cell subsets become available, making personalized medicine a reality in contemporaneous cancer treatment. The identification of specific phenotypes and activation markers for MDSC may improve the prediction ability of the test described in this study. These results highlight the importance of linking the frequency of immune suppressive cells with clinical outcome.
Bacterial chemotaxis control process analysis with SysML

Field: Computer Science (Physical Sciences)

Abstract This paper looks at the bacteria chemotaxis control process utilizing the System Modeling Language (SysML) to leverage well‐defined and proven engineering tools for architecting, analyzing, and refining complex systems. It proposes a new methodology called reverse‐engineering object‐oriented systems engineering method (RE‐OOSEM) that converts descriptive biology research information into descriptive systems engineering information. It utilizes SysML and model‐based systems engineering (MBSE) to capture system architecture from biological system knowledge and inputs them into systems engineering tools. From an engineering point of view, this allows greater insight into how biological systems operate and suggests how much model detail is required to uncover a top‐down system understanding. RE‐OOSEM methodology guides the SysML chemotaxis control capture process. SysML syntax is used instead of biological syntax to facilitate biological chemotaxis control system analysis from an engineered system point of view. The model can act as a scaffolding to help uncover system function, the relationships of system components and processes, and bioinformatic phenotype and genotype correlation. An executable MathWorks Stateflow chemotaxis control process model based on the SysML architectural model is included. The results show the following engineering perspective observations. (1) Several control components are not dedicated but are available and utilized when needed. (2) Individual chemoreceptors act together as a sensor array. (3) Phosphate groups act as a signaling mechanism. (4) Methylation via CH 3 groups of the chemoreceptor results in sensitivity adaptation. (5) Closed‐loop control collaboratively utilizes ligand bonding, phosphorylation, and methylation. (6) Timing relationships of the control subprocesses give insight into the system's architecture.
A Life Less Ordinary: Socio-economic aspects of adult congenital heart disease

Field: Medicine (Health Sciences)

The dramatically improved survival and clinical outcomes of children with congenital heart disease (CHD) has allowed attention to shift towards less basic, but nevertheless very important other issues influencing course of life of adults with CHD. This includes aspects of education, employment and career, personal development, relationships and offspring, insurability, lifestyle, quality of life and the chance to develop other diseases. Care for adults with CHD should therefore not only comprise care for survival and medical treatment, but also include attention for socio-economic aspects and the challenges that are thereby faced. To be able to provide such care, more insight into these aspects is needed. Unfortunately, attention within the medical field for socio-economic outcomes is still limited. This thesis describes several studies that were conducted to gain more insight in socio-economic aspects of adults with CHD.
How tonicity regulates gene expression.

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

The expression of a number of different mammalian genes is directly affected by hypertonicity. At present, the list of their products includes aldose reductase, heat shock proteins, early response factors, and transporters for betaine, inositol, and taurine. Hypertonicity increases the abundance of the mRNAs for all of them. Aldose reductase mRNA levels increase because of increased transcription with little change in the stability of its mRNA. Transcription of the betaine transporter also increases. The mechanisms by which hypertonicity increases the transcription of these mammalian genes remain speculative. However, the consideration of transcriptional control of betaine transport in bacteria and of heat shock proteins in many organisms provides interesting insight into this question.
Chromohalobacter salexigens sp. nov., a moderately halophilic species that includes Halomonas elongata DSM 3043 and ATCC 33174.

Field: Immunology and Microbiology (Life Sciences)

Two strains that were originally isolated and characterized as members of the moderately halophilic species Halomonas elongata, strains DSM 3043 (= 1H11) and ATCC 33174 (= 1H15), were studied in detail. Their complete 16S rRNA sequences were determined and, when compared to sequences available from the databases, they showed a close phylogenetic relationship to Chromohalobacter marismortui. In addition, DNA-DNA hybridization experiments showed that both strains are members of the same species, but their DNA relatedness to the type strains of Halomonas elongata, ATCC 33173T, and Chromohalobacter marismortui, ATCC 17056T, is very low. Phenotypically, the two strains showed very similar features, related to those of Chromohalobacter, but clear differences were found between these two strains and Chromohalobacter marismortui. On the basis of these data, it is proposed that Halomonas elongata DSM 3043 and ATCC 33174 should be included in a new species of the genus Chromohalobacter, Chromohalobacter salexigens sp. nov. The type strain is DSM 3043T (= ATCC BAA-138T = CECT 5384T = CCM4921T = CIP106854T = NCIMB 13768T).
Experiments for determination of species of field-collected lab-rared mosquitoes using near-infrared spectroscopy (A1T1)

Field: Agricultural and Biological Sciences (Life Sciences)

Experiments for determination of species of field-collected lab-rared mosquitoes using near-infrared spectroscopy (A1T1) This dataset contains near-infrared spectroscopy (NIRS) measurements on mosquitoes of different species (Anopheles arabiensis, Anopheles coluzzii, Anopheles gambiae) collected from different locations in Burkina Faso (Dioulassoba, Klesso, Longo) at larval stage, and reared in the lab together with colony mosquitoes of the same species. For further details on the experimental setup see: P.M. Esperança, A.M. Blagborough, D.F. Da, F.E. Dowell, T.S. Churcher (2018) "Detection of Plasmodium berghei infected Anopheles stephensi using near-infrared spectroscopy". Parasites and Vector, 11:377. https://doi.org/10.1186/s13071-018-2960-z. The structure of the data file is as follows: column 1 (Scan_ID): scan identifier column 2 (Mosquito_ID): mosquito identifier column 3 (Position): scanning position identifier (1,2,3,4) column 4 (Location): collection location ("Dioulassoba", "Klesso", "Longo") column 5 (Generation): generation type ("Lab", "F0", "F1") column 6 (Species): mosquitoes species ("arabiensis", "coluzzii", "gambiae") columns 7 to 2157 (x350 to x2500): NIRS absorbance measurements for wavelengths in the range 350 to 2500 nanometers
Identifying minimal number of seed influencers in social networks

Field: Computer Science (Physical Sciences)

Social networks are prevalent. They contain large pools of users whom exist in communities. While a social network could seem harmless with the mere participation of human beings, there should not be an underestimate towards the influence a social network can exert. Social media today has had vast impact on our culture, ideologies and beliefs. Not only has it changed the way we think, it has also affected the way we communicate and socialized on the Web. The effect that social media has caused, can either aid the society or harm it by circulating negative or unhealthy ideas to any community. In other words, social media has the ability to infect (with negative ideas) or purify the communities (with positive benefits to aid growth). These effect spans from boosting business economy to changing views on politics to socialization to cyber bullying as well as to invasion of privacy; much less, anything can be done via utilizing the social media (network). Thus, if social networks could influence the communities and eventually the world to a better future, the benefits obtained could be out of this world. Hence, it is often useful to identify nodes that exert more influences over the other nodes. These nodes could be the keys to generate the large influence over multiple communities. This project aims to develop software tools for such purposes via a web-based application, designed for analytical users only since this information would be useful for government officials or business executives that wish to exert the some (positive) influence over the network. This application would be able to filter and pick the most influential node(s) based on centrality algorithms. Subsequently, a selected group of nodes could very well generate a large influence of more than a certain percentage, also known as Coverage Percentage (CP). The application user would have a CP he/she wants to achieve in mind. Via the use of the product application, the user would be able to select each node, one at a time, such that he/she could revise the CP after each subsequent node. The aim of the application is to filter possible subsequent nodes so that the final CP achieved would meet his/her aim of CP.
Living together: The phenomenon of house occupancy in Indonesia with particular reference to Balikpapan East Kalimantan

Field: Social Sciences (Social Sciences)

Abstract This study explores housing problem concerning the most widely perceived idea of housing needs that heavily influenced by the technical and macro-scale level as well as the units’ tenure and occupancy which is mainly perceived as owning and renting. On the other hand, the housing cannot be seen as such due to the existence of different context of the problem and the various aspirations of occupants. This research highlights the other kind of occupancy phenomenon among Indonesian who can get access to and live in a housing unit without owning or renting – by living and staying with their relatives. In particular reference to Balikpapan East Kalimantan, this study concerns the modus of this specific kind of house occupancy and aims to reveal the housing processes as well as aspirations of the house occupants who live and stay together.
SEC-C-U: The Security of Intensive Care Unit Medical Devices and Their Ecosystems

Field: Health Professions (Health Sciences)

An intensive care unit (ICU) is dedicated to caring for patients whose medical condition places them at high risk of mortality or serious morbidity. ICU medical devices (ICUMDs) are used to closely monitor, stabilize, and treat ICU patients who are often unconscious and rely almost solely on ICUMDs. ICUMDs have become more autonomous, with a range of components, connectivity to external devices, and functionalities, opening the door to cyber-attacks. We present a taxonomy based on the functionality of 19 widely used ICUMDs, providing an explanation of each device's medical role, properties, interactions, and how they impact each other's security. We provide an extensive survey of 16 possible attacks aimed at ICUMDs and assess each device's vulnerability. We also create an ecosystem graph describing the roles and interactions of the players of each ICU sub-department. For each device type we produce a unique attack flow diagram that presents the most vulnerable vectors and components within the ecosystem. Finally, we survey relevant security mechanisms and map their coverage for the attacks, identifying existing gaps. We show that current security mechanisms generally fail to provide protection, covering just 12.5-56.3% of the attacks against ICUMDs, leaving the devices and the patients vulnerable.
Seborrhoeic dermatitis: current treatment practices

Field: Medicine (Health Sciences)

Seborrhoeic dermatitis (SD) is a recurrent, chronic inflammation of the skin that occurs on sebum rich areas such as the face, scalp and chest, characterised by red scaly lesions. The are many studies indicating that Malassezia yeasts play an important role in the aetiology of this condition, most of the evidence for which comes from demonstrated responsiveness to treatment with antifungal agents. Its aetiology, however, is far from being resolved. Some believe that it is the immune response of the skin to the Malassezia that is the cause of the disease. Traditional treatments of SD have been the use of keratolytic agents or corticosteroids. Since the discovery of ketoconazole, a considerable amount of research has been focused on determining the efficacy of various antifungal agents. This article reviews clinical trial data on treatment options available for SD.
Importance of a Holistic Stakeholder Participation Model in Community Development

Field: Social Sciences (Social Sciences)

Using the Mapungubwe World Heritage site case, this chapter emphasises the importance of a holistic stakeholder participation model in sustainable community development. In addition, it seeks to establish stakeholders' perspectives within the context of this study. Stakeholder participation is preferred as an effective model because it has proven to enhance effectiveness of policies by integrating stakeholder knowledge and perceptions, and builds support for policies through increased transparency, accountability and legitimacy of decision-making only if it well drafted and well implemented. Sequential mix-method was adopted for this chapter. This chapter established that a holistic stakeholder participation model is important in community development for Mapungubwe descendant community, owing to the belief that park management does not take them seriously. In conclusion, the findings and results validate each other, supporting the proposed Mapungubwe World Heritage Site stakeholder participation model.