jimnoneill/paper-to-field-training huggingface dataset:
Computer Aided Kinematic Design and Analysis

Field: Engineering (Physical Sciences)

In the motion analysis of the coupler points of a four-bar mechanism, one can achieve reproductive results graphically for the displacement, but it is very time consuming. However, when the velocity and acceleration are determined graphically, the results are not very accurate. Rather than obtaining reproducible results one often gets an average value with a plus or minus around this value. Reproducible results are always received for the analysis of the displacement, velocity and acceleration of a coupler point using a digital computer. Since the computer, under normal conditions, stores a number which may have up to eight decimal places, one can be certain that the results will be accurate to as many significant figures as the input numbers are.\nAs was mentioned earlier in plotting the center-point curve, a complete curve can be plotted graphically from one opposite pole quadrilateral. With four specified positions of a body, there are three distinct opposite pole quadrilaterals and therefore the complete center-point curve can be plotted three times. When this is done graphically, it is very difficult to achieve on curve, rather, the results are more likely to be a “band” or three distinct curves which are very close. This is significant because for the included example in the appendix one opposite side was 20 units long and yet the computer solution resulted in one curve for three plots.\nThe program as presented may very well be improved upon by changing a part or parts of them. Although the center-point curve can be plotted from one quadrilateral, for this thesis results can be received from all three quadrilaterals. Since the complete curve can be plotted from one quadrilateral, two quadrilaterals could be eliminated from the program in order to save compiling time. The center-point curve results are not capable of being plotted by a computer curve plotter as they appear in this program; however, with a few changes one could adapt this program to a curve plotter.\nAdvisor: James C. Wolford
Staphylococcus borealis sp. nov., isolated from human skin and blood

Field: Immunology and Microbiology (Life Sciences)

When analysing a large cohort of Staphylococcus haemolyticus , using whole-genome sequencing, five human isolates (four from the skin and one from a blood culture) with aberrant phenotypic and genotypic traits were identified. They were phenotypically similar with yellow colonies, nearly identical 16S rRNA gene sequences and initially speciated as S. haemolyticus based on 16S rRNA gene sequence and MALDI-TOF MS. However, compared to S. haemolyticus , these five strains demonstrate: (i) considerable phylogenetic distance with an average nucleotide identity <95 % and inferred DNA–DNA hybridization <70 %; (ii) a pigmented phenotype; (iii) urease production; and (iv) different fatty acid composition. Based on the phenotypic and genotypic results, we conclude that these strains represent a novel species, for which the name Staphylococcus borealis sp. nov. is proposed. The novel species belong to the genus Staphylococcus and is coagulase- and oxidase-negative and catalase-positive. The type strain, 51-48 T , is deposited in the Culture Collection University of Gothenburg (CCUG 73747 T ) and in the Spanish Type Culture Collection (CECT 30011 T ).
Serum 25-Hydroxyvitamin D Level Is Not Associated with Duration and Activity of Disease in Melanoma Patients

Field: Medicine (Health Sciences)

Preclinical and epidemiological studies showed the association between 25-hydroxyvitamin D (vitamin D) and cancer development. The aim of the study was to evaluate serum vitamin D levels of melanoma patients and compare them with other malignancies and healthy controls. A total of 87 cutaneous melanoma patients from a tertiary cancer center were included in the study. Vitamin D levels were measured with electrochemiluminescence binding assay. There were no differences between serum vitamin D levels of melanoma patients, other malignancies and healthy controls (median values: 18.8, 14.3, and 24.5 ng/ml, respectively, p > 0.05). Vitamin D deficiency (<20 ng/ml) was found in 56% of melanoma patients and 42% of healthy controls; however serum vitamin D levels in only 16% of both melanoma patients and healthy controls were sufficient (>30 ng/ml) (p > 0.05). Furthermore, no difference regarding serum vitamin D levels was found between melanoma and other malignancies. Age, gender and clinical stage were not found statistically correlated with serum vitamin D levels. Similarly, serum vitamin D level was not associated with disease duration and presence or absence of active disease. In conclusion, there was no difference between serum vitamin D levels of melanoma patients and healthy controls and it was also not associated with duration and activity of disease.
The efficacy of probiotics on the prevention of pouchitis for patients after ileal pouch-anal anastomosis: A meta-analysis

Field: Medicine (Health Sciences)

BACKGROUND: To date, a few studies indicated that probiotics are beneficial to pouchitis, but no meta-analyses summarized the outcomes of probiotics in pouchitis in detail. OBJECTIVE: This meta-analysis discusses probiotics in the prevention of pouchitis for patients after ileal pouch-anal anastomosis (IPAA) and the relationship between probiotics preventive effect and the duration of therapy and history. METHODS: PubMed, EMBASE and Cochrane Library databases were searched from inception until February 2022. Risk ratio (RR), mean difference (MD) and their 95% confidence interval (CI) were analyzed by Review Manager 5.3. The subgroup analysis was also performed to explore the agent for influencing outcomes. RESULTS: A total of 8 studies were included in this meta-analysis. The incidence of pouchitis in probiotics was significantly lower than that in the control (RR = 0.19, 95%CI [0.12, 0.32], P⁢ï⁢¼⁢ 0.00001), and the PDAI (pouchitis disease activity index) in probiotics was also significantly lower (MD =-5.65, 95%CI [-9.48, -1.83]). After the subgroup analysis, we found that probiotics work better in the short-term (RR = 0.12, 95%CI [0.04, 0.40], P= 0.0004), but may not achieve the desired effect in the long-term (RR = 1.20, 95%CI [0.40, 3.60], P= 0.75). CONCLUSIONS: Probiotics are beneficial in the prevention of pouchitis after IPAA, especially in the short-term.
Epidemiological Evaluation of Next-Generation Sequencing and MLPA Results in Patients with a Presumptive Cystic Fibrosis Diagnosis

Field: Medicine (Health Sciences)

Cystic fibrosis is an autosomal recessive disease caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The spectrum and frequencies of CFTR mutations vary among populations. As a result of continuous migration around the world, the frequency of CF variants may change and is still unclear in some geographies. We aimed to define the CFTR gene variants we observed as a result of our single-center experience. This research assessed the outcomes of 353 patients who underwent next-generation sequencing to identify variations in the CFTR gene. Variants classified as clinically uncertain significance, likely pathogenic or pathogenic detected in patients with pre-diagnosis of cystic fibrosis who underwent genetic testing were included in the evaluation. The variants detected in the vast majority of cases were comparable to those found in other populations. However, some variants showed significant differences in allele frequencies when compared to European and Asian populations. Mutations were detected in 25.2% of cases. This dataset revealed that the most common mutations in patients presenting to our center were c.2991G&gt;C, c.2856G&gt;C, c.1545_1546delTA, c.1521_1523 del and c.202A&gt;G. This research presents data on CFTR variations to determine the frequency of CF in the Istanbul province of our nation and to identify additional frequently occurring pathogenic variants that are currently unknown. This kind of research has the potential to facilitate the creation of a localized strategy for maximizing healthcare provision for individuals with CF.
Gut associated lymphoid tissue: a morphological and immunocytochemical study of the human appendix.

Field: Medicine (Health Sciences)

Gut associated lymphoid tissue in 15 normal appendices has been characterised in tissue sections using both morphological criteria and immunocytochemical techniques. A panel of monoclonal and polyclonal antibodies was used including antibodies to B-cells, T-cells, macrophages, HLA DR and immunoglobulins. The lymphoid tissue in the appendix was shown to bear a strong resemblance to that in lymph nodes with the exception of the region where the appendix follicles associate with the dome epithelium, which has no lymph node equivalent. This zone of cells between the lymphoid follicles and the dome epithelium termed the 'mixed cell zone' has been shown to contain an abundance of HLA DR-bearing cells, some of which have irregular nuclear morphology and resemble follicle centre cells. These cells were seen to extend into the epithelium of the dome but not the crypts. Using a monoclonal anti-B-cell antibody a population of B-cells was detected in the equivalent areas of mixed cell zone and epithelium and quantitative studies showed that these intraepithelial B-cells comprised approximately 4-5% of the cells in the epithelium. The mixed cell zone was also seen to contain T-cells, S-100 protein-containing macrophages and occasional lysozyme-containing macrophages. Plasma cells were rarely seen in this area.
Investigation of the impact of RBC aggregation on RBC retention by macrophages under hypoxia.

Field: Medicine (Health Sciences)

<p>A Snapshot of RBCs adhering to macrophages from experiments and simulations. SIM1 represents the simulations considering the aggregation between sickle RBCs, while SIM2 does not. B The plot depicts the number of RBCs adhered to the macrophages over time for experimental and simulation studies. (C-D) The plots describe the two possible adhesion mechanisms that regulate the RBC adhesion to the macrophages (C, cluster filtration) and (D, transitive filtration).</p>
The Generalized Frankel Conjecture in Sasaki Geometry

Field: Mathematics (Physical Sciences)

Journal Article The Generalized Frankel Conjecture in Sasaki Geometry Get access Weiyong He, Weiyong He 1Department of Mathematics, University of Oregon, Eugene, OR 97403, USA Correspondence to be sent to: whe@uoregon.edu Search for other works by this author on: Oxford Academic Google Scholar Song Sun Song Sun 2Department of Mathematics, Imperial College, London SW7 2AZ, UK Search for other works by this author on: Oxford Academic Google Scholar International Mathematics Research Notices, Volume 2015, Issue 1, 2015, Pages 99–118, https://doi.org/10.1093/imrn/rnt185 Published: 06 September 2013 Article history Received: 13 November 2012 Revision received: 12 April 2013 Accepted: 05 August 2013 Published: 06 September 2013
[MR imaging of adrenal masses smaller than 5 cm. Characterization with T2 relaxation time at 1.5 T].

Field: Medicine (Health Sciences)

The T2 relaxation times of 28 adrenal masses smaller than 5 cm obtained using a 1.5 Tesla MR imaging system were analysed to evaluate the ability of this parameter to characterize the tissue masses. The adrenal masses included 13 nonhyperfunctioning adenomas, five hyperfunctioning adenomas, five metastatic tumors, two pheochromocytomas, one nodular hyperplasia, one ganglioneuroma, and one cyst. The mean T2 value of nonhyperfunctioning adenomas was almost the same as that of hyperfunctioning adenomas. A significant difference was found in T2 (p less than 0.01) between nonhyperfunctioning adenoma (50 msec +/- 7 msec; mean +/- S.D.) and metastatic tumor (63 msec +/- 11 msec), whereas there was no significant difference in mass size between them. The two pheochromocytomas and the ganglioneuroma, which were derived from adrenal medulla, had relatively long T2 of over 70 msec. The T2 values of nodular hyperplasia and adrenal cyst were 58 msec and 123 msec, respectively. Although the T2 values of metastatic tumors tended to be longer than those of nonhyperfunctioning adenomas, differentiation between them with a T2 of 60 msec was not necessarily possible, especially in smaller masses. The T2 values of two metastatic tumors of less than 2 cm indicated 50 msec levels. There seemed to be a correlation between mass size and T2 in metastatic tumors. In adenomas, however, no significant correlation was demonstrated. We conclude that the characterization of small adrenal masses by T2 at 1.5 Tesla is unsatisfactory in differentiating metastatic tumors from nonhyperfunctioning adenomas.
Best-Response Dynamics in Local Public Good Games

Field: Decision Sciences (Social Sciences)

In this paper we study the convergence of the best-response dynamics in a class of potential games that are played on a network. The games we consider have linear best-responses and exhibit strategic substitutes. A prominent member of this class is the local public good game introduced in Bramoulle and Kranton (2007) and further examined in Bramoulle, Kranton and d'Amours (2014). In these games, the structure of Nash equilibria can be very complex, due to high multiplicity (continuum of equilibria often appear). The convergence of best- response dynamics in these games has been studied in the particular case where equilibria are isolated. Here, we consider the general problem and treat the case where continuum of equilibria appear. First, we show that the best-response dynamics converges to the set of Nash equilibria with probability one. Next, we retrieve the results about isolated equi- libria as a special case. In particular, in the case of pure public goods, we show that interior Nash equilibria are unstable, while among the set of specialized Nash equilibria, those that are stable are those which form a maximal independent set of order at least 2 in the network where the game is played. We then turn to the case with continuum of equilibria, and provide necessary and sucient conditions under which a component of Nash equilibria is an attractor of the dynamics. The conditions are as follow: if a component is an attractor, then it necessarily contains specialised Nash equilibria, that are extreme points of the component, in some sense. Then, in order to check whether the component is an attractor or not, it is sucient to focus on these specialized equilibria. At every specialized equilibria, we then consider the subgraph induced by the set of inactive players that are linked to only one active individual. The component is an attractor of the dynamics if and only if this subgraph is a union of complete components. This is a very sharp result because it relates the set of attractors of the dynamics to the topology of the network, and it does so in a way that is very simple to operate. Additionally, it helps rule out entire components of Nash equilibria (those that are not attractors) and gives us a better understanding of where individuals might converge to in games that are plagued by multiplicity.
Physical Implications of the Sub-threshold GRB GBM-190816 and its Associated Sub-threshold Gravitational Wave Event

Field: Physics and Astronomy (Physical Sciences)

The LIGO-Virgo and Fermi collaborations recently reported a possible joint detection of a sub-threshold gravitational wave (GW) event and a sub-threshold gamma-ray burst (GRB), GBM-190816, that occurred 1.57 s after the merger. We perform an independent analysis of the publicly available data and investigate the physical implications of this potential association. By carefully studying the following properties of GBM-190816 using Fermi/GBM data, including signal-to-noise ratio, duration, f-parameter, spectral properties, energetic properties, and its compliance with some GRB statistical correlations, we confirm that this event is likely a typical short GRB. Assuming its association with the sub-threshold GW event, the inferred luminosity is $1.47_{-1.04}^{+3.40} \times 10^{49}$ erg s$^{-1}$. Based on the available information of the sub-threshold GW event, we infer the mass ratio q of the compact binary as $q=2.26_{-1.43}^{+2.75}$ according to the reported range of luminosity distance. If the heavier compact object has a mass > 3 solar masses, q can be further constrained to $q=2.26_{-0.12}^{+2.75}$. The leading physical scenario invokes an NS-BH merger system with the NS tidally disrupted. Within this scenario, we constrain the physical properties of such a system to produce a GRB. The GW data may also allow an NS-BH system with no tidal disruption of the NS or a BH-BH merger. We apply the charged compact binary coalescence (cCBC) theory (for both a constant charge and an increasing charge for the merging members) to derive the model parameters to account for GBM-190816 and found that the required parameters are extreme. Finally, we argue that the fact that the observed GW-GRB delay time scale is comparable to that of GW170817/GRB 170817A suggests that the GW-GRB time delay of these two cases is mainly defined by the time scale for the jet to propagate to the GRB emission site.
Impact on quit attempts of mailed general practitioner &apos;brief advice&apos; letters plus nicotine replacement therapy vouchers

Field: Health Professions (Health Sciences)

AIM: To test whether a personalised letter from general practitioners advising their patients who are smokers to quit, together with an exchange card for one month of nicotine gum, prompts them to make quit attempts, is acceptable and feasible. METHODS: Non-randomised before–after ecological study involving general practices in Auckland, New Zealand. Personalised letters with exchange cards for four weeks of nicotine gum were sent to 831 patients within a single Auckland health board area who were recorded as current smokers on their general practitioner’s files. The comparison group was the population in another Auckland health board area. We measured calls to Quitline and vouchers redeemed at pharmacies from both areas before and after the intervention. Follow-up surveys of recipients and general practitioners assessed acceptability. RESULTS: Quitline calls from baseline to the end of the intervention from the intervention district compared with a comparison district were not significantly higher (5%, 95% CI -2–12%, p=0.195), but nicotine replacement therapy (NRT) voucher redemptions were significantly higher (9%, 95% CI 3–16%, p=.005). Almost 9% of the exchange cards were redeemed for NRT. Despite initial difficulties in accurately identifying smokers from their records, responding GPs found the strategy very acceptable. DISCUSSION: The strategy shows potential as a simple way to increase the number of smokers making supported quit attempts through primary care. In the light of the urgent need to increase cessation rates, a randomised trial of this promising approach is warranted. KEYWORDS: Smoking cessation; Quitline, nicotine replacement therapy; general practice; brief advice
1,2,5-Thiadiazole-1-oxides. II. The Chemistry of the Amines

Field: Chemistry (Physical Sciences)

Amino-subatitured 1,2,5-thiadiazolel-oxides farm salts with Naone or Nan.These reacted wirh alkyl halides.acyl chlorides, isocyanares and methyl aerylafe to afford ring nitrogen svbsfituted products.The 3-amino, 4-ethoxy analog participates in a self condensation wirh KOB to form bis-~hiadierolopyrazine oxide dipotasaium salt.Alkylarion of this with benzyl brwide afforded a
Proton pump inhibitors long term use‐trends and patterns over 15 years of a large health maintenance organization

Field: Health Professions (Health Sciences)

Abstract Background Proton pump inhibitors (PPI) are used for a variety of indications. Despite reported associations with undesirable effects, their long‐term use is on the rise, while appropriate indications, dose, and treatment duration may deviate from guideline recommendations. Objectives Primary to examine the annual patterns of PPI use. Secondary‐ to assess indications for initiating PPI treatment, long‐term use, and factors associated with long‐term use in a large Israeli health maintenance organization. Methods A historical cohort study of 528 420 eligible PPI users during 2000–2015, analyzed PPI use using defined daily doses and the proportion of patients covered method. Data on indications for treatment initiation, clinical and socio‐demographic parameters were captured as well. A multivariable logistic‐regression model was used to identify factors associated with long‐term use of PPI. Results The annual incidence rates of patients initiating PPI treatment were relatively constant, ranging between 2.4% and 3.1% of the adult population, with a monotonic increase in annual consumption and prevalence (reaching 12.7% in 2015). Reflux, functional symptoms, and Helicobacter pylori eradication were the most common indications for initiating PPI therapy. However, 27% of patients had no recorded indication for treatment. Fifteen percent of patients used PPI for over 6 months, especially in older age groups. Conclusions Utilization of PPI increases steadily, mainly due to chronic use. Prolonged consumption is associated with specific clinical indications and older age. Health organizations should encourage awareness of appropriate use among physicians, specifically in the elderly, patients with reflux, and those with functional disorders.
Outbreak of Salmonella enteritidis phage type 1 infection in British tourists visiting Mallorca, June 1996

Field: Medicine (Health Sciences)

Three British tourists became ill while on holiday in the same hotel in Alcudia, Mallorca from 11 to 25 June 1996; Salmonella enteritidisinfections were diagnosed upon their return to England. An environmental health officer informed the Gastrointestinal
Data from Genetic Aberrations Leading to MAPK Pathway Activation Mediate Oncogene-Induced Senescence in Sporadic Pilocytic Astrocytomas

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

<div>Abstract<p><b>Purpose:</b> Oncogenic BRAF/Ras or NF1 loss can potentially trigger oncogene-induced senescence (OIS) through activation of the mitogen-activated protein kinase (MAPK) pathway. Somatic genetic abnormalities affecting this pathway occur in the majority of pilocytic astrocytomas (PA), the most prevalent brain neoplasm in children. We investigated whether OIS is induced in PA.</p><p><b>Experimental Design:</b> We tested expression of established senescence markers in three independent cohorts of sporadic PA. We also assessed for OIS <i>in vitro</i>, using forced expression of wild-type and V600E-mutant BRAF in two astrocytic cell lines: human telomerase reverse transcriptase (hTERT)-immortalized astrocytes and fetal astrocytes.</p><p><b>Results:</b> Our results indicate that PAs are senescent as evidenced by marked senescence-associated acidic β-galactosidase activity, low KI-67 index, and induction of p16<sup>INK4a</sup> but not p53 in the majority of 52 PA samples (46 of 52; 88.5%). Overexpression of a number of senescence-associated genes [<i>CDKN2A</i> (<i>p16</i>), <i>CDKN1A</i> (<i>p21</i>), <i>CEBPB</i>, <i>GADD45A</i>, and <i>IGFBP7</i>] was shown at the mRNA level in two independent PA tumor series. <i>In vitro</i>, sustained activation of wild-type or mutant BRAF induced OIS in both astrocytic cell lines. Loss of p16<sup>INK4a</sup> in immortalized astrocytes abrogated OIS, indicative of the role of this pathway in mediating this phenomenon in astrocytes. OIS is a mechanism of tumor suppression that restricts the progression of benign tumors. We show that it is triggered in PAs through p16<sup>INK4a</sup> pathway induction following aberrant MAPK activation.</p><p><b>Conclusions:</b> OIS may account for the slow growth pattern in PA, the lack of progression to higher-grade astrocytomas, and the high overall survival of affected patients. <i>Clin Cancer Res; 17(14); 4650–60. ©2011 AACR</i>.</p></div>