jimnoneill/paper-to-field-training huggingface dataset:
An RT-PCR-based multi-gene prognostic signature predicts distant metastasis of node negative, ER positive breast cancer from FFPE sections

Field: Medicine (Health Sciences)

506 Background: Gene expression profiles have been shown to predict distant metastasis risk in breast cancer patients. For routine medical practice, molecular prognostic tests need to be able to quantify metastasis risk with readily available samples and optimally employ regulatory-approved platforms. Methods: 142 early stage, N-, ER+, untreated breast cancer patients were chosen. Mean age was 61.8 (31 - 89) yrs with 72% > 55 yrs. RNA was isolated from 4×10 μm FFPE sections. Using real-time RT-PCR, 200 genes selected from van ‘t Veer et al, Dai et al, Paik et al and additional candidate genes were profiled. Primary endpoint was distant metastasis free survival. A prognostic signature was identified using semi-supervised principal component method. Metastasis score (MS) was calculated from gene expression levels. Results: We identified a unique 15-gene prognostic signature and 3 normalization genes. Probability of metastasis for any time period can be calculated from MS and was evaluated for 2, 5, and 10 yrs. Using median of MS to stratify patients, the high-risk group had a hazard ratio (HR) of 4.1 (95%CI 1.77–9.54, p = 0.001) vs. the low-risk group. 5-yr and 10-yr metastasis free survival rates (std. error) were 0.76 (0.053) and 0.62 (0.064) in the high-risk group and 0.96 (0.025) and 0.90 (0.038) in the low-risk group. Multivariate Cox regression analyses indicated that molecular signature had independent prognostic value with HR of 2.97 (95%CI 1.17 - 7.52, p = 0.022) after adjusting for age, tumor size and grade. Molecular signature was more prognostic in the low-grade subgroup (HR = 6.85, 95%CI 1.81–25.88) than an unstratified analysis. AUC at 5 yr was 0.65 and 0.60 for molecular signature and Adjuvant Online (AO) respectively. The prognosticator combining both had AUC of 0.67. 10-yr metastasis probabilities from MS and AO have low correlation (R 2 =0.17). Conclusions: A prognostic signature based upon mRNA expression of 15 genes has been identified using FFPE sections with RT-PCR for early stage, N-, ER+ patients. Metastasis score that quantifies distant metastasis risk for any time period, not confounded with any treatment effect, can help clinicians and patients to choose among different therapeutic options. (Lau and Wang contribute equally) [Table: see text]
Pathological changes produced by coronary embolization with metallic mercury in the dog.

Field: Veterinary (Health Sciences)

Pathological studies of myocardium at intervals up to one year after embolization of the left circumflex coronary artery in dogs have shown that the changes are those of a granulomatous myocarditis and arteritis rather than infarction, and suggest that this technique does not provide a suitable model for the study of acute infarction or chronic ischaemic heart disease.
Spindle cell rhabdomyosarcoma of the prostate

Field: Medicine (Health Sciences)

Abstract The spindle cell rhabdomyosarcoma is a rare variant of the embryonal rhabdomyosarcoma, mostly occurring in childhood. Only a few cases are described in adults. To date, no case of the spindle cell subtype of the prostatic embryonal rhabdomyosarcoma has been published. We report on a 23‐year‐old man, initially presenting with obstructive micturition problems, perineal pain and night sweat. After diagnosis by transrectal biopsy of the prostate, radiochemotherapy within the CWS 2002 P study was applied: nine cycles of vincristine, doxorubicin, actinomycin D, ifosfamide, and fractionated radiotherapy of the tumor and suspect lymph nodes (final dose 50.4 G y). The tumor initially shrank, but an early local recurrence arose. Second‐line chemotherapy was applied, followed by a salvage radical cytoprostatectomy. The patient died of disseminated disease 14 months after diagnosis.
Effects of indomethacin on brain blood flow, cerebral metabolism, and sagittal sinus prostanoids after hypoxia

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

We tested the hypotheses that during recovery from hypoxia, newborn piglets exhibit a posthypoxic cerebral hyperemia, indomethacin-pretreated piglets exhibit a posthypoxic cerebral hypoperfusion, and that the changes caused by indomethacin are dose dependent and related to the loss of prostanoids. We studied piglets exposed to 40 min of hypoxia after pretreatment with high (5 mg/kg, n = 9) or low (0.3 mg/kg, n = 8) doses of indomethacin or placebo (n = 9) and allowed to recover for 120 min. In the placebo and low-dose pretreatment groups, total and regional brain blood flow increased during hypoxia but returned to baseline 10 min after hypoxia. High-dose indomethacin pretreatment was associated with a posthypoxic hypoperfusion to certain brain regions at 10 min of recovery to values similar to those after indomethacin treatment before the onset of hypoxia. During and after hypoxia, the cerebral metabolic rate of oxygen was preserved in both the placebo and low-dose groups and decreased significantly during hypoxia in the high-dose group. Sagittal sinus prostacyclin was reduced significantly in both indomethacin-treated groups throughout the study. We conclude that a posthypoxic hyperemia is not observed in newborn piglets. This finding was not altered by pretreatment with a therapeutic dose of indomethacin, whereas a pharmacological dose was associated with selective hypoperfusion to certain brain regions both before hypoxia and during recovery from hypoxia.
A conjoint study of quantitative and semi‐quantitative assessment of failure in a strudel manufacturing plant by means of FMEA and HACCP, Cause and Effect and Pareto diagram

Field: Chemical Engineering (Physical Sciences)

Summary Failure Mode and Effect Analysis (FMEA) model was applied for the risk assessment of strudel manufacturing. A tentative approach of FMEA application to the strudel industry was attempted in order to identify the potential failures in the flow diagram and to compare them with the critical control points in the strudel processing. Preliminary Hazard Analysis was employed towards analysing and predicting the occurring failure modes in a food chain system (strudel processing plant), based on the functions, characteristics and/or interactions of the ingredients or the processes, upon which the system depends. Critical control points were identified and implemented in the Cause and Effect diagram (also known as Ishikawa, tree diagram and fishbone diagram) in order to reveal the underlying causes of failures. Finally, Pareto diagrams were employed in an attempt to optimise the detection potential of FMEA.
On the 1/D expansion for directed polymers

Field: Mathematics (Physical Sciences)

We present a variational approach for directed polymers in $D$ transversal dimensions which is used to compute the corrections to the mean field theory predictions with broken replica symmetry. The trial function is taken to be a symmetrized version of the mean-field solution, which is known to be exact for $D=\infty$. We compute the free energy corresponding to that function and show that the finite-$D$ corrections behave like $D^{-4/3}$. It means that the expansion in powers of 1/D should be used with great care here. We hope that the techniques developed in this note will be useful also in the study of spin glasses.
Gaussian Mixture Decomposition of Time-Course DNA Microarray Data

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

In this chapter we present the decomposition approach to the analysis of large gene expression profile data sets. We address the problem of analysis of transient time-course data of expression profiles. We accept the assumption that co-expression of genes can be related to their belonging to the same Gaussian component. We assume that parameters of Gaussian components, means and variances, can differ between time instants. However, the gene composition of components is unchanged between time instants. For such problem formulations we derive the appropriate version of expectation-maximization algorithm recursions for the estimation of model parameters.We apply the derived method to the data on gene expression profiles of human K562 erythroleukemic cells and we discuss the obtained gene clustering.
A human RNA helicase-like protein, HRH1, facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome.

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

Because the nuclear export of mRNA occurs only after the splicing reaction is completed, intron-containing pre-mRNA does not normally appear in the cytoplasm. As a mechanism to secure this, intron-containing RNA is retained in the nucleus via formation of the spliceosome. Therefore, the process of releasing spliced mRNA from the spliceosome after completion of splicing is an essential step for triggering the nuclear export of the spliced mRNA. In budding yeast, RNA helicase-like protein Prp22 is implicated in this process. Here we demonstrate the function of HRH1, a human protein homologous to Prp22, in mammalian cells using dominant-negative HRH1++ mutants (dn-HRH1). dn-HRH1 protein stalls on the spliceosome and prevents release of the spliced RNA from the spliceosome in vitro. Expression of dn-HRH1 in mammalian cells leads to inhibition of splicing and to extensive nuclear export of unspliced pre-mRNA, probably because of the incapability of recycling spliceosome components that normally retain the pre-mRNA in the nucleus. The arginine/serine-rich domain (RS domain) of HRH1, which is missing in Prp22, confers a nuclear localization signal, and appears to facilitate the interaction of HRH1 with the spliceosome. This is the first report on a bona fide mammalian homolog of yeast Prp splicing factor, and also on a mammalian RNA helicase-like splicing factor.
Effects of Temperature on the Development and Survival of Metriona Elatior (Coleoptera: Chrysomelidae) Immatures

Field: Agricultural and Biological Sciences (Life Sciences)

The larval developmental rate of the tortoise beetle Metriona elatior Klug (Coleoptera: Chrysomelidae), a potential biocontrol agent of tropical soda apple (TSA) Solanum viarum Dunal (Solanaceae), was studied in the laboratory at 3 constant temperatures (20[degree], 25[degree], and 30[degree]C), photoperiod (14:10 L: D), and relative humidity 60%- 80% in growth chambers. Sixteen neonate larvae were individually reared on excised TSA leaves placed in 0.5-liter transparent-plastic containers for each temperature treatment. Larvae were daily checked to determine the number and duration of larval instars at each of the temperature tested. At 20[degrees] and 25[degree]C, the percent survival from first instar to adult was 75 and 73%, respectively. A constant temperature of 30[degrees]C had a detrimental effect on the larvae and none reached the pupa/adult stages. The general life cycle of this beetle is discussed.
The Effect of Alumina Nanoparticles on Increasing the Lifespan of Aged XLPE MV Cable Insulations

Field: Materials Science (Physical Sciences)

This study presents a method for rejuvenation, life elongation and Restoration of XLPE cables insulation by a silicone rejuvenation fluid containing alumina nanoparticles. The rejuvenation fluid included a type of silane coupling agent and alumina (aluminum oxide) nanoparticles. The silane coupling agents react with the water in the cable insulation and water tree regions, remove the water molecules and dry the cable insulation. In this way, they fill the water tree voids and bond the alumina nanoparticles with polymer matrix of the cable and improve the dielectric properties of the cable. After injecting the rejuvenation fluid into the aged XLPE cables, tanδ test was repeated on rejuvenated samples every week for one month and its variations were compared with new and aged samples. Microstructural analysis of the aged and rejuvenated samples was carried out and compared by SEM microscope. FTIR analysis evaluates and compares the chemical bonds in the rejuvenated and aged cable insulations. EDX spectroscopy determined the type and amount of absorbed elements on the rejuvenated sample surface. The impact of rejuvenation fluid on aged XLPE cables was determined according to the 4 mentioned tests.
Improved integrated structural control design using covariance control parameterization

Field: Engineering (Physical Sciences)

This paper investigates multiobjective integrated control/structure design using covariance control to parameterize the controller. An advantage of this approach is that the control objectives can be specified as a set of competing analytical goals or constraints instead of a single scalar cost function. From this formulation, a multiobjective numerical optimization problem is formulated to execute the integrated control-structure design. The performance of this approach is investigated on a simple disturbance rejection problem in which the control objectives and the structural design objectives conflict. The integrated design optimization both increases control performance and decreases the structural mass with a counterintuitive design. In addition, these results add to previous work that demonstrates the protential of integrated design optimization of structures and controllers. It then appears that when the structure and controller are considered simultaneously, the resulting combination is an improved design. However, the extent of the design improvement is apparently problem dependent.
Surface treatment against bromine defectivity in plasma etch reactor

Field: Chemical Engineering (Physical Sciences)

This paper evaluates two treatment processes to reduce HBr in plasma etch reactor. The bromine concentration is measured by a total X-Ray fluorescence (TXRF) technique. The first treatment is based on an outgassing effect by heating and the second on a plasma etch surface treatment. Both treatments can lead to a reduction by a factor 20 of the bromine concentration. The electrical impact of the plasma needs to be evaluated.
[Multicystic renal dysplasia with ectopic implantation of the ureter in boys. Apropos of 6 cases].

Field: Medicine (Health Sciences)

The prevalence of multicystic dysplastic kidney has increased since the development of antenatal ultrasound diagnosis. Even though, the rarity of symptomatic forms and case reports of spontaneous regressions antenatally or after postnatal ultrasound follow-up have reduced indications of nephrectomy which is less and less appropriate. However, discovery of ectopic ureteric implantation in boys makes certain additional investigations as intravenous pyelography, cystography and ultrasound, essential before making any therapeutic decision. Nevertheless, some cases remain undescriptible. In these cases, operative opacification of any patent ureter can provide more precise information about ureteric implantation. Lastly, only a dissection and resection as complete as possible of any patent ureter and pelvic cystic dilatation can prevent subsequent complications.
Identification of Immunogenic and Virulence-Associated Campylobacter jejuni Proteins

Field: Immunology and Microbiology (Life Sciences)

ABSTRACT With the aim of identifying proteins important for host interaction and virulence, we have screened an expression library of NCTC 11168 Campylobacter jejuni genes for highly immunogenic proteins. A commercial C. jejuni open reading frame (ORF) library consisting of more than 1,600 genes was transformed into the Escherichia coli expression strain BL21(DE3), resulting in 2,304 clones. This library was subsequently screened for immunogenic proteins using antibodies raised in rabbit against a clinical isolate of C. jejuni ; this resulted in 52 highly reactive clones representing 25 different genes after sequencing. Selected candidate genes were inactivated in C. jejuni NCTC 11168, and the virulence was examined using INT 407 epithelial cell line and motility, biofilm, autoagglutination, and serum resistance assays. These investigations revealed C. jejuni antigen 0034c (Cj0034c) to be a novel virulence factor and support the usefulness of the method. Further, several antigens were tested as vaccine candidates in two mouse models, in which Cj0034c, Cj0404, and Cj0525c resulted in a reduction of invasion in spleen and liver after challenge.
V, v connection cophase power supply system based on active power filter

Field: Engineering (Physical Sciences)

Considering the problems existed in the electric traction power supply system of electrified railway, such as the severe three-phase unbalance, abundant harmonic wave and reactive power, and in particular, neutral section insulator between adjacent power supply sections, a new type of cophase traction power supply system is built by combining V, v connection transformer with active filter and AT power supply. In this system, one secondary line winding with a middle tap of V, v connection transformer is connected with AT traction electric network. The other secondary line winding is connected through active filter. In this way, each power supply section has the same voltage and consequently neutral section insulator can be removed. The measured cophase comprehensive compensation current is regarded as the reference to control active filter, eliminate three-phase unbalance, and filtrate harmonic wave and reactive power. Simulation has validated the correctness and the feasibility of this cophase power supply system which is applicable to high-speed electrified railway.
Power quality disturbance detection based on IEWT

Field: Engineering (Physical Sciences)

With the continuous development of distributed generation, power quality problems are more complex. In order to ensure that the power quality of the active distribution network meets the requirements of users, it is of great significance to accurately obtain the power quality disturbance parameters. For the problem that the traditional empirical wavelet transform needs to manually select the number of frequency bands when analyzing unknown power quality disturbances, this paper proposes an improved empirical wavelet transform (IEWT) algorithm. The algorithm uses the Piecewise Cubic Hermite Interpolation (PCHIP) method and the improvement of the transition region to achieve adaptive frequency band division and noise interference reduction, and different amplitude (AM) and pitch (FM) components can be obtained. Then the Normalized Direct Quadrature (NDQ) algorithm and Singular Value Decomposition (SVD) algorithm are used to extract frequency, amplitude and time parameters of the AM-FM components. Simulation and experimental results show that the power quality disturbance parameters extracted by the proposed method are more accurate and less affected by noise.
Genome-wide association study of leprosy in Malawi and Mali

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

Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae . Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3 . We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10 −9 ; OR = 0.51 [95% CI 0.40 − 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
Visualization of kinetochores and analysis of their refractility in crane-fly spermatocytes after aldehyde fixation

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

Glutaraldehyde and formaldehyde were used to fix crane-fly spermatocytes for observation with differential interference contrast (DIC) microscopy. In aldehyde-fixed cells, kinetochores exhibit contrast not normally observed in living cells. Although the mechanism underlying this result is not understood, the visualization of kinetochores as distinct refractile objects opens the way for analysis of unstained kinetochores with the light microscope. The analysis of kinetochore refractility reported in this paper is made possible by the finding that the refractility of chromosomes in formaldehyde-fixed cells decreases as the concentration of formaldehyde is increased. In 4% formaldehyde, the refractility of chromosomes is matched with that of its surround, chromosomes appear invisible, and kinetochores may be analyzed as if chromosomes were not present. Kinetochores were imaged with DIC optics, and then digital image analysis was performed. Gray-level scans through the highlight and shadow of an individual kinetochore parallel to the axis of shear resulted in a curve having a slope proportional to the DIC optical path gradient. Curves from autosomal kinetochores imaged in anaphase had slopes approximately one-half those recorded at metaphase under identical optical conditions. By contrast, kinetochore thicknesses (defined as the distance between the peak and the valley of a gray-level scan) at those two stages were not significantly different. These data suggest a loss of dry mass from autosomal kinetochores during anaphase. Neither the refractility nor thickness of lagging sex kinetochores varied as autosomes went through anaphase. The conclusion drawn from these findings is that the decreased refractility of autosomal kinetochores in anaphase is movement-related. Cell Motil. Cytoskeleton 40:147–159, 1998. © 1998 Wiley-Liss, Inc.
Long-Legged Girls and the Transnational Circuits of Vietnamese Popular Culture

Field: Arts and Humanities (Social Sciences)

On a balmy summer evening, the crowds for Vu Ngoc Dang's Nhung Co Gai Chan Dai, or Long-Legged Girls (2004), at the Korean-owned Diamond Plaza in Ho Chi Minh City were enormous. Sleek motorbikes were stacked in rows around the mall; throngs of young, fashionable people animatedly congregated to meet for drinks and watch the latest film. Comprising four floors devoted to various consumerist pleasures, the mall is flanked by tall business towers and lies adjacent to the Notre Dame Cathedral and a national park, at night a notorious meeting place for lovers and for prostitutes and their clients. Diamond Plaza offers foreigners and an emerging Vietnamese middle class an air-conditioned respite from the heat during the summer months. It remains a place of leisure for a well-heeled generation of Vietnamese youth, also called the "@ generation."