jimnoneill/paper-to-field-training huggingface dataset:
A case of mucosa-associated lymphoid tissue (MALT) lymphoma arising in the accessory parotid gland

Field: Medicine (Health Sciences)

A 62-year-old female visited our hospital complaining of a swelling in her right cheek. Computed tomography (CT) revealed a well-demarcated solid tumor, 2 × 2 cm in size, on the outer side of the right masseter muscle, located apart from the parotid gland. We suspected malignant lymphoma using fine-needle aspiration cytology, and an open biopsy was performed. Histologically, proliferation of atypical small cleaved lymphocytes was seen around the enlarged lymph follicles. Residual salivary duct epithelium was detected within the lesion. In immunohistochemical staining, these tumor cells were positive for CD20, CD79a and bcl-2, but not positive for CD10, CD3, and CD45RO. We diagnosed the tumor as mucosa-associated lymphoid tissue (MALT) lymphoma arising in an accessory parotid gland. According to the histological diagnosis, radiotherapy was done and the patient had complete remission. However, forty-three months after treatment, she had a recurrent tumor in the inguinal lymph node.
Identification of putative regulatory signals including the HAP1 binding site in the upstream sequence of the Aspergillus nidulans cytochrome c gene (cycA).

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

We speculate that a HAP1-like protein, similar to those which regulate oxygen transcriptional activation of many yeast respiratory genes, will probably also regulate the A. nidulans cytochrome c (cycA) gene. As part of a study to investigate the significance of a putative HAP1 (Haem Activator Protein) binding site in the regulatory region of the cycA gene, routine sequencing revealed an error in the published sequence (Raitt et al. 1994 Mol. Gen. Genet. 242: 17-22). Examination of the corrected sequence, including RT-PCR analysis of cycA mRNA, showed that an extra intron was present, and that the published translational start site was incorrect. This meant that the putative HAP1-binding site proposed by Raitt et al. could not be a regulatory element. However, further sequence analysis of the upstream sequence of the corrected cycA gene revealed putative regulatory signals, including possible HAP1 binding sites which are a closer match to recently reported yeast consensus sequences (Ha et al. 1996 Nucl. Acids Res. 24: 1453-1459).
Two-Group Comparison Of Gene Signatures: Failure Of Conventional Statistical Methods And Validation Of A Novel Algorithm

Field: Computer Science (Physical Sciences)

The gene expression profiling could aid the physicians to better understand the cellular morphology, resistance to chemotherapy and overall clinical outcome of disease [1,2]. Such individualized treatment may significantly increase survival due to the optimization of treatment procedure according to clinical pathogenesis. Ein-Dor et al [3] have pointed out that the gene sorted for the same clinical types of patients but different groups differed widely and possessed only few genes in common. An explanation to this lack of overlap between predictive signatures from different studies with the same goal may be due to the presence of more predictive genes than required to design an accurate predictor [4]. However, the microarray technique itself has been shown to be highly reproducible within and across two high volume laboratories [5]. Numerous statistical procedures including t-test [6,7], analysis of variance [8], Pearson correlation [9], Wilcoxon signed-rank test [10,11] and Mann Whitney U test [12,13] have been used for comparison of microarray data. However, the validity of various conventional statistical methods for two-group comparison of gene signatures was never evaluated using carefully selected data sets. A novel algorithm with software support is presented herein for more realistic and comprehensive interpretation of gene signatures.
Measurement-based control approach for tuning PID controllers: application to induction machines

Field: Engineering (Physical Sciences)

This paper presents an approach to design proportional - integral – derivative controllers for induction machines using measurements. Most control methods developed for induction machines are generally based on mathematical models. Due to complex dynamics of induction machines, identified models are often unable to perfectly describe their behaviour. Thus, the system performance will be limited by the quality of the identified model. Hence, developing control methods that do not require the availability of system model is advantageous. Here, we propose an approach that uses the frequency response data to directly design controllers. The main idea here is to find controller parameters so that the closed-loop frequency response fits a desired frequency response. Its main advantage is that errors associated with the modelling process are avoided. Moreover, the control design process does not depend on the order and complexity of the plant. A practical application to induction machines illustrates the efficacy of the proposed approach.
Fat-Related surface tension and wetting properties of milk

Field: Agricultural and Biological Sciences (Life Sciences)

The surface tension of milk was found to decrease logarithmically with time, regardless of fat content. Moreover, the surface tension decreased with fat content up to about 35 g.kg-1. Above 10 MPa, homogenization resulted in increased surface tension, probably due to the lower creaming and lack of caseins in the continuous phase. The initial contact angle of homogenized milk on glass was similar to that of skim milk, probably due to the presence of casein micelles on the globule surface. After the first immersion, skim milk wetted glass surfaces completely. Conversely, the contact angle of whome milk increased with time, suggesting the formation of a hydrophobic adborption layer on glass. The composition and conformation of this layer can affect fouling and cleaning in technological dairy processes involving fat globules.
Development and Application of an IAC-PCR Kit for the Rapid Detection of Salmonella spp.

Field: Immunology and Microbiology (Life Sciences)

【Objective】The purpose of this study was to develop a rapid and accurate detection kit for Salmonella spp.using polymerase chain reaction(PCR) with an internal amplification control(IAC).【Method】 The specific primers and IAC were designed according to the conserved genes invA and stn in Salmonella spp.The optimization of the components and the evaluation of the parameters for the kit were carried out in this study.【Result】 The experiment indicated that the specific 362 bp DNA fragment was amplified against 147 reference strains of Salmonella spp.,while 28 strains of non-Salmonella only showed the 520 bp amplified band of IAC.The detection limit of the kit for purified genomic DNA was 8.0 fg/PCR.It was confirmed in artificial contamination assay that Salmonella spp.could be detected by the kit after 8-10 h enrichment when 4-5 CFU germs were inoculated in 10 mL milk.Thirty food samples were detected by the IAC-PCR kit in this study,and the experiments demonstrated that IAC could successfully indicate false-negative results.Besides,the kit worked well after being frozen-thawed for 60 times or stored at-20℃ for one year.【Conclusion】The IAC-PCR detection kit developed in this study has good performances in specificity,sensitivity,stability and accuracy and is suitable for the rapid and accurate detection of Salmonella spp.
Clinical Significance of Down-Regulated CD70 and CD27 Expression in Poor Prognosis of Esophageal Squamous Cell Carcinoma [Retraction]

Field: Medicine (Health Sciences)

Shan T, Zhao X, Zhang Z, et al. Cancer Manag Res.&amp;nbsp; 2020;12:6909&amp;ndash; 6920.\nAt the request of the authors, the Editor-in-Chief and&amp;nbsp;Publisher of Cancer Management and Research wish to&amp;nbsp;retract the published article.\nFollowing a review of their recently published article the&amp;nbsp;authors identified some errors in the methods and reporting&amp;nbsp;which led to inconsistencies in the reported data.&amp;nbsp;Specifically:â The mRNA expression of CD70 and CD27 was&amp;nbsp;detected using 153 esophageal squamous cell carcinoma&amp;nbsp;(ESCC) samples from this study. However,&amp;nbsp;only 59 (Figure 1A) and 43 (Figure 1B) paired samples&amp;nbsp;were selectively displayed in Figure 1;â In total, 126 ESCC patient samples were used to&amp;nbsp;detect the protein levels of CD27 and CD70 by&amp;nbsp;immunohistochemistry (IHC). However, only 50&amp;nbsp;samples were selectively displayed in the article in&amp;nbsp;Figure 2.â Some sample information was lost which led to the&amp;nbsp;incorrect reporting of patient data numbers for&amp;nbsp;Figure 2G.\nThe editor has determined the findings in the paper are no&amp;nbsp;longer valid and agreed with the authors request to retract&amp;nbsp;the article.\nThe authors wish to apologise for this error.\nOur decision-making was informed by our policy on publishing&amp;nbsp;ethics and integrity and the COPE guidelines on&amp;nbsp;retraction.\nThe retracted article will remain online to maintain the&amp;nbsp;scholarly record, but it will be digitally watermarked on&amp;nbsp;each page as &amp;ldquo;Retracted&amp;rdquo;.This retraction relates to this paper\n&amp;nbsp;
The Nature of Occupational Stress Among Public Defenders

Field: Social Sciences (Social Sciences)

AbstractHard quantitative research about occupational stress among public defenders is rare. Given the central role of public defenders in the courts, research is desperately needed to identify the most aggravating stressors plaguing public defenders. Two hundred and seventeen public defenders in New York State ranked various potential stressors by frequency and intensity. Stressors that occurred with both high frequency and high intensity were having too much work; not knowing when a case might be called into trial; having no defense if a case were called; satisfying conflicting parties; dealing with upset clients and their families; arguing with prosecutors; and having no trial options because of harsh sentences. Though some of these stressors come with the territory, such reforms as caseload reduction, docket reform, and increased judicial tolerance for trials could bring some relief.
Basics of beer brewing process and related alcohol chemistry - An old beer in a new bottle

Field: Chemistry (Physical Sciences)

Beer is one of the favorite beverages produced by the fermentation of grains. The global production figures indicate an increasing trend during the last decade. This article highlights the beer brewing process, chemistry concepts involved, and problems and prospects. The emphasis is on conceptual understanding of both theory and practice, and the chemical perspectives and possibilities to provide an appreciation of alcohol chemistry exposure in our daily lives that have particular significance and several positive effects to enrich the learning experience.
[Metastases of human tumor cells in immunosuppressed newborn rats].

Field: Medicine (Health Sciences)

The metastatic ability of human tumour cells can easily be evaluated by using as an experimental model the production of metastases in newborn rats immunosuppressed by an optimal dose of anti-thymocyte serum. Thus, following sub-cutaneous injection of 10(6) cells, a human melanoma cell line, tumorigenic but non metastatic in nude mice, produces within 3 weeks tumours in all inoculated rats and lymph node and pulmonary metastases in 50% of the animals. The cloning of this cell line in semi-solid agar shows its heterogeneity and demonstrates that it contains poorly tumorigenic but highly metastatic cells.
[Serological evaluation of the prevalence of Pneumocystis jirovecii infection in children with respiratory tract infections in Poland].

Field: Medicine (Health Sciences)

In the years 1998-2008 there were examined for pneumocystosis serum samples collected from 5223 children with respiratory tract infections, aged up to 10 years. The examinations were carried out for the presence of specific IgG and IgM antibodies with an indirect immunofluorescent antibody test. Specific anti-Pneumocystis antibodies were detected in 68,7% of the examined children, including 68,49% with IgG and 2.85% with IgM antibodies. The highest percentages of IgM and IgG positive samples were encountered, respectively, in children aged up to 6 months (4,17%) and in those in the second half of the first year of life (73%). The results of the examinations indicated that in Poland the prevalence of pneumocystosis in children with symptoms of respiratory tract infection is similar to that described by foreign authors for healthy, immunocompetent children.
Image Charge Detection for Deterministic Ion Implantation

Field: Physics and Astronomy (Physical Sciences)

Image charge detection is presented as a possible candidate to realise deterministic ion implantation. The deterministic placement of single impurities in solid substrates will enable a variety of novel applications, using their quantum mechanical properties for sensors or qubit registers.\nIn this work, experimental techniques are used together with theoretical calculations to develop, characterise and optimise the detection of charged objects in a single pass through an image charge detector. In the main experimental part, ion bunches are employed as a model system for highly charged ions in proof-of-principle measurements with detector prototypes built in our labs. Image charge signals are characterised in the time and frequency domain. Using a statistical measurement and data analysis protocol, the noise and signal probability density functions are determined to calculate error and detection rates. It was found that even at an extremely low signal-to-noise ratio of 2, error rates can be suppressed effectively for high fidelity implantation. Aiming to improve the sensitivity, the maximum possible signal-to-noise ratio is calculated and discussed in dependence on the design parameters of an optimised image charge detector and the kinetic ion parameters. Lastly, a new ion implantation set-up combining focused ion beam technology with a source able to produce highly charged ions is introduced.
The “Uselessness” of the Triune God

Field: Arts and Humanities (Social Sciences)

The Triune God’s intrinsically glorious singularity and experiences of its gracious presence and the objective reality of “evils” and experiences of horrendous suffering are both “mysteries.” Both are “unmanageable” by human creatures. The appropriate initial response to each is silence. They differ in that God’s concrete reality is intrinsically a “positive” mystery a se that cannot be comprehensively “grasped” cognitively or “explained,” whereas particular “evils” are “negative” mysteries crying out for explanations leading to their eradication. If “positive mystery” is not acknowledged, it may be hoped that moral and natural evils can all be “explained” and eliminated. So their “mystery” is not intrinsic. If “positive mystery” is acknowledged, the concrete actuality of “negative evils” is itself an a-rational and inexplicable reality. Because God is intrinsically “mystery” God cannot be the causal explanation of the reality of “negative mysteries.” God is not a useful “explanatory hypothesis.” The singularity of God’s intrinsic glory entails God’s intrinsic “uselessness.”
Can Protein Diffusion in Membranes Sense Cell Environment

Field: Physics and Astronomy (Physical Sciences)

We study protein diffusion in multicomponent lipid membranes close to a rigid substrate separated by a layer of viscous fluid. The large-distance, long-time asymptotics for Brownian motion are calculated using a nonlinear stochastic Navier-Stokes equation including the effect of friction with the substrate. The advective nonlinearity, neglected in previous treatments, gives only a small correction to the renormalized viscosity and diffusion coefficient at room temperature. We find, however, that in realistic multicomponent lipid mixtures, close to a critical point for phase separation, protein diffusion acquires a strong power-law dependence on temperature and the distance to the substrate $H$, making it much more sensitive to cell environment, unlike the logarithmic dependence on $H$ and very small thermal correction away from the critical point.
DNA Barcoding of Shark Meats Identify Species Composition and CITES-Listed Species from the Markets in Taiwan

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

<div><p>Background</p><p>An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan’s fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits.</p><p>Methods</p><p>In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan.</p><p>Results</p><p>Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, <i>Alopias pelagicus, Carcharhinus falciformis</i>, <i>Isurus oxyrinchus,</i> and <i>Prionace glauca</i> consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of <i>Sphyrna</i>, <i>C. longimanus</i> and <i>Carcharodon carcharias</i>.</p><p>Conclusion</p><p>DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.</p></div>
EFFET DE L'INOCULATION SUBSÉQUENTE DU VIRUS SV40 SUR LA TRANSPLANTATION DE CELLULES TRANSFORMÉES PAR CE VIRUS

Field: Medicine (Health Sciences)

The inoculation of SV 40 virus during the few days following the transplantation of SV 40 -transformed cells to adult hamsters inhibits the development of the transplanted tumors. The number and the size of the tumors are markedly reduced relative to those developing in control animals inoculated with medium 199.The animals that were resistant to the first transplantation, and those where the tumors were excised, showed an increased resistance to a second transplantation effected after an interval of 8 months.These results are interpreted as supporting the view that the transplantation of virus-transformed cells, and the development of the transplanted tumor, induce complex immunological reactions. The homologous oncogenic virus can be used to modify favorably the balance between cellular and humoral immune reactions conducive to the development of the tumor.
Unconventional Fluorescence Quenching in Naphthalimide-Capped CdSe/ZnS Nanoparticles

Field: Chemistry (Physical Sciences)

Core–shell (CS) CdSe/ZnS quantum dots (QD) capped with ligands that possess a mercapto or an amino group and a naphthalimide (NI) as chromophore unit, linked by a short ethylene chain (CS@S–NI and CS@H2N–NI, respectively), have been synthesized and fully characterized by infrared and nuclear magnetic resonance spectroscopies, high-resolution transmission electron microscopy, and voltammetry as well as by steady-state absorption and emission spectroscopies. The organic ligands HS–NI and H2N–NI act as bidentate ligands, thereby causing a drastic decrease in the QD emission. This was particularly evident in the case of CS@S–NI. This behavior has been compared with that of commercially available QDs with octadecylamine as the surface ligand and a QD capped with decanethiol ligands (CS@S–D). The interaction between the anchor groups and the QD surface brings about different consequences for the radiative and nonradiative kinetics, depending on the nature of the anchor group. Our results suggest that the naphthalimide group "stabilizes" empty deep trap states due to the carbonyl group capacity to act as both a σ-donor and a π-acceptor toward cations. In addition, the thiolate group can induce the location of electron density at shallow trap states close to the conduction band edge due to the alteration of the QD surface provoked by the thiolate binding.
Design And Investigation Of A Modular Focused Collimator Based Multiple Detector Ring System For SPECT Imaging Of The Brain

Field: Medicine (Health Sciences)

The ability of focused collimators to achieve both high sensitivity and high resolution at depth makes them highly desirable for SPECT imaging. Tomographic systems with stationary detector rings are known to have the advantages of simplicity, stability and tolerance to variations in detector response. We have combined these two desirable features in the design of a multidetector ring SPECT system with a unique modular focused collimator for brain imaging. In a manner similar to that employed by 4th generation CT scanners, each detector unit acquires a set of fan beam projection data while the collimator assembly makes a complete rotation. Our investigation shows that the new tomograph can be expected to achieve a spatial resolution of 8 mm and a system sensitivity of 2,500 cps/pCi/cc for a 13 mm thick image slice. The high performance characteristics of the new SPECT system should make it a useful tool in functional imaging of the brain, especially in perfusion studies using the current 1-123 or Tc-99m labeled agents.
Effects of down-regulation of HAX1 protein on apoptosis of Hela cells

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

Objective To investigate the effect of the down-regulation of HAX1 protein on maintenance of mitochondria membrane potential and apoptosis of Hela cells.Methods After 3 days of inhibiting the expression of HAX1 protein by using RNAi technology,the changes in mitoehondria membrane potential of Hela cells were observed and compared between experimental group and control group by JC-I labeling method and flow cytometry.Three h after addition of H2O2(2 retool/L)to induce apoptosis,the apoptosis rate was detected by using Annexin V-FITC technique.Results The decreasing percent of cellular mitochondria membrane potential in control and experimental groups was 9.52%and 21.12%in average respectively(P＜0.05).The H2O2(2 mmol/L)-induced apoptosis rate in control and experimental groups was 21.80%and 31.73%in average respectively(P＜0.05).Conclusion Down-regulation of HAX1 protein can not only reduce the stability of mitochondria membrane potential,but also induce apoptosis of Hela ceils.

Key words:
RNA interference; Mitoehondria; Membrane potential; Apoptosis