gebhart/patrepeval huggingface dataset:
Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features (2016)

Lung cancer is the most prevalent cancer worldwide, and histopathological assessment is indispensable for its diagnosis. However, human evaluation of pathology slides cannot accurately predict patients' prognoses. In this study, we obtain 2,186 haematoxylin and eosin stained histopathology whole-slide images of lung adenocarcinoma and squamous cell carcinoma patients from The Cancer Genome Atlas (TCGA), and 294 additional images from Stanford Tissue Microarray (TMA) Database. We extract 9,879 quantitative image features and use regularized machine-learning methods to select the top features and to distinguish shorter-term survivors from longer-term survivors with stage I adenocarcinoma (P<0.003) or squamous cell carcinoma (P=0.023) in the TCGA data set. We validate the survival prediction framework with the TMA cohort (P<0.036 for both tumour types). Our results suggest that automatically derived image features can predict the prognosis of lung cancer patients and thereby contribute to precision oncology. Our methods are extensible to histopathology images of other organs.
Members of a low‐copy number gene family encoding glutamyl‐tRNA reductase are differentially expressed in barley (1996)

In plants tetrapyrrole synthesis is initially light regulated on the level of 5-aminolevulinate (ALA) synthesis. ALA is formed from glutamate in three enzymatic steps. Glutamyl tRNA reductase (GluTR) catalyses the NADPH-dependent reduction of glutamyl tRNA to glutamate 1-semialdehyde. GluTR is encoded by a low-copy gene family consisting of three to four genes. Three different cDNA clones are presented. Full-length clones BHA1 and 87 differ in the length of the 3' untranslated region and code for a 58.5 kDa protein. The sequence of the partial clone, BHA13, contains at least 87 base mismatches in the coding region for the mature GluTR resulting in 11 amino acid substitutions. Synthesis of a recombinant mature and a truncated GluTR lacking the first 19 amino terminal amino acids in Escherichia coli lead only in the latter case to complementation of an E. coli hemA mutant. Steady-state level of BHA1- and BHA13-specific mRNA encoding GluTR were analysed by Northern blot hybridization using cDNA-specific oligo nucleotides and quantitative reverse transcriptase-polymerase chain reaction. Accumulation of the two RNA species is light induced in greening barley and controlled during cellular development. In contrast to BHA13, BHA1 transcripts are present in roots and are elevated after cytokinin treatment of dark-grown seedlings. Furthermore, BHA1 mRNA shows oscillation under circadian growth conditions. GluTR transcript levels correlate with the capacity for ALA synthesis indicating that the rate-limiting substrate flux through the ALA synthesizing pathway can be at least partially attributed to GluTR expression. Consequences of the initial control of the chlorophyll metabolic pathway on the level of ALA formation are discussed.
Pilot clinical studies of long duration, low intensity therapeutic ultrasound for osteoarthritis (2014)

Osteoarthritis is one of the leading causes of disability in the aging population. Long duration, low intensity therapeutic ultrasound has had promising impact in animal models to slow the progression of the disease and provide joint relief. Two pilot studies were conducted using a novel, wearable platform for delivering ultrasound to evaluate the potential clinical benefits of ultrasound therapy on knee osteoarthritis. There was a pain reduction effect from using ultrasound, as high as fifty two percent in one study. As well, initial data demonstrates that mobility may be increased for patients experiencing mild to moderate arthritis of the knee.
Human T-cell lymphotropic virus type 1 (HTLV-1)-induced syncytium formation mediated by vascular cell adhesion molecule-1: evidence for involvement of cell adhesion molecules in HTLV-1 biology (1997)

While studying the potential role of vascular cell adhesion molecule-1 (VCAM-1) in infection of endothelial cells by human immunodeficiency virus (HIV), we found that VCAM-1 can mediate human T-cell lymphotropic virus type 1 (HTLV-1)-induced syncytium formation. Both expression-vector-encoded and endogenously expressed VCAM-1 supported fusion of uninfected cells with HTLV-1-infected cells. Fusion was obtained with cell lines carrying the HTLV-1 genome and expressing viral proteins but not with an HTLV-1-transformed cell line that does not express viral proteins. In clones of VCAM-1-transfected cells, the degree of syncytium formation observed directly reflected the level of VCAM-1 expression. Syncytium formation between HTLV-1-expressing cells and VCAM-1+ cells could be blocked with antiserum against HTLV-1 gp46 and with a monoclonal antibody (MAb) against VCAM-1. Fusion was not blocked by antiserum against HIV or a MAb against VLA-4, the physiological counter-receptor for VCAM-1. The results indicate that VCAM-1 can serve as an accessory molecule or potential coreceptor for HTLV-1-induced cell fusion and provide direct evidence of a role for cell adhesion molecules in the biology of HTLV-1.
Cyclodextrins in drug delivery (2005)

Cyclodextrins are a family of cyclic oligosaccharides with a hydrophilic outer surface and a lipophilic central cavity. Cyclodextrin molecules are relatively large with a number of hydrogen donors and acceptors and, thus, in general they do not permeate lipophilic membranes. In the pharmaceutical industry cyclodextrins have mainly been used as complexing agents to increase aqueous solubility of poorly soluble drugs, and to increase their bioavailability and stability. Studies in both humans and animals have shown that cyclodextrins can be used to improve drug delivery from almost any type of drug formulation. However, the addition of cyclodextrins to existing formulations without further optimisation will seldom result in acceptable outcome. Currently there are approximately 30 different pharmaceutical products worldwide containing drug/cyclodextrin complexes on the market.
Universal classes of hash functions (Extended Abstract) (1977)

This paper gives an input independent average linear time algorithm for storage and retrieval on keys. The algorithm makes a random choice of hash function from a suitable class of hash functions. Given any sequence of inputs the expected time (averaging over all functions in the class) to store and retrieve elements is linear in the length of the sequence. The number of references to the data base required by the algorithm for any input is extremely close to the theoretical minimum for any possible hash function with randomly distributed inputs. We present three suitable classes of hash functions which also may be evaluated rapidly. The ability to analyze the cost of storage and retrieval without worrying about the distribution of the input allows as corollaries improvements on the bounds of several algorithms.
A pathway for the biosynthesis of straight and branched, odd- and even-length, medium-chain fatty acids in plants. (1994)

Pathways and enzymes of fatty acid synthase-mediated, long-even-chain (generally C16-C20) fatty acid synthesis are well studied, and general metabolism involved in short-chain (C4-C7) fatty acid biosynthesis is also understood. In contrast, mechanisms of medium-chain (C8-C14) fatty acid synthesis are unclear. Recent work suggests involvement of chain-elongation-terminating thioesterases in medium-chain fatty acid formation in oilseeds and animals. We have shown that iso- and anteiso-branched and straight, odd- and even-length, short-chain fatty acids esterified in plant-trichome-gland-produced sucrose esters are synthesized by using carbon skeletons provided by modified branched-chain amino acid metabolism/catabolism. The principal enzymes involved are those catalyzing leucine biosynthesis in all organisms and those leading to short-chain alcohols in mutant yeasts and alkyl acids in Clostridium species (products often serving as mammalian pheromones). Here we provide evidence that C10-C12 straight medium-chain and C10-C12 branched medium-chain acyl acids of tomato, C6-C8 straight-chain acyl acids of Petunia, and C6 and C8 branched acyl acids of Nicotiana glutinosa are formed by alpha-ketoacid elongation without participation of fatty acid synthase-mediated reactions or -independent thioesterases. This different metabolism suggests greater integration of amino acid and fatty acid metabolism than previously considered and provides other avenues to study and manipulate not only straight even-length but also odd- and even-length straight and branched medium-chain fatty acid biosynthesis.
Endothelial release of tissue-type plasminogen activator and ischemia-induced vasodilatation are linked in patients with coronary heart diseaseM (1999)

Dysfunction in the vascular endothelium disturbs blood flow and predisposes individuals to atherosclerosis. Deteriorated fibrinolysis may further enhance the risk for atherothrombosis. We investigated 14 healthy volunteers and 24 patients with coronary heart disease. Endothelium-dependent (acetylcholine- and ischemia-induced) and endothelium-independent (nitroprusside-induced) vasodilatation in the forearm vasculature were studied using strain-gauge plethysmography, and the fibrinolytic system measured as the response of tissue plasminogen activator (t-PA) to provocation testing (20 min venous occlusion; VOT). When acetylcholine-induced vasodilatation was measured, endothelium-dependent vasodilatation differed between groups: those with coronary heart disease had a median value of 8.5 ml/min per 100 g tissue (25th to 75th percentile 4.8-10.3), compared with 11.6 ml/min per 100 g tissue (7.3-15.5) among healthy volunteers (P = 0.03). However, ischemia-induced vasodilatation showed no difference between the groups [26.8 (22.7-35.0) versus 29.1 (25.6-30.7) ml/min per 100 g tissue, respectively, NS]. Levels of t-PA after VOT also showed no difference between the groups [21.5 (16.5-31.9) versus 20.4 (11.8-31.5) ng/ml, respectively, NS]. Results of ischemia tests and levels of t-PA after VOT correlated only in patients with coronary heart disease (r = 0.5, P = 0.015), and not in healthy volunteers. We observed a positive correlation between endothelium-dependent vasodilatation function and endothelial release of t-PA. This indicates that the same mechanism that results in defective ischemia-induced endothelial relaxation in patients with coronary heart disease may also result in suppressed fibrinolytic capacity, thus making such patients more prone to atherothrombosis.
In situ hybridization study of PSP94 (prostatic secretory protein of 94 amino acids) expression in human prostates (1999)

BACKGROUND The prostatic secretory protein of 94 amino acids (PSP94), also named β-microseminoprotein, is one of the major proteins secreted by the human prostate. However, its value as a prognostic marker for prostate cancers is still under debate. The aim of the present study was to examine the expression pattern of this protein in fetal, pubertal, and aged human prostates. METHODS Nonisotopic in situ hybridization using a digoxigenin-labeled riboprobe for PSP94 and immunohistochemistry were used to demonstrate the expression of PSP94 in different regions or zones of fetal, pubertal, and adult human prostates. Its localization pattern was also compared with those of two other major secretory proteins, prostate-specific antigen (PSA) and prostatic acid phosphatase (PAP), by immunohistochemistry. RESULTS PSP94 mRNA and its protein were localized to the secretory epithelium of normal pubertal and adult human prostates. No hybridization signal and immunoreactivity of PSP94 were seen in fetal prostates at 6–7 months of gestation, whereas some glandular cells were positive to PSA and PAP immunostainings. In the adult prostates, PSP94 expression was intense in the acini in the peripheral zone, less intense in the transition zone, and variable in the central zone. Such a zonal expression pattern was more apparent in the pubertal prostates. However, no obvious differential expression pattern was observed in the immunohistochemistry of PAP and PSA, which showed a uniform staining of the secretory epithelia of the acini in all anatomic zones. The hybridization signals and immunoreactivity of PSP94 became reduced or lost in premalignant prostatic intraepithelial neoplastic lesions and different grades of prostatic carcinomas. CONCLUSIONS Fetal prostates at 6–7 months of gestation already synthesize PSA and PAP but not PSP94. The delayed expression of PSP94 appears to correlate with the development of the prostate gland. A differential expression pattern of PSP94 is demonstrated in different anatomical zones, showing that this protein is more expressed and synthesized in the acini in the peripheral zone than in the central and transition zones. However, such a zonal pattern is not seen in the immunohistochemistry of PSA and PAP. The present study also shows that PSP94 is downregulated in different grades of prostate cancers. Prostate 41:99–109, 1999. © 1999 Wiley-Liss, Inc.
Complement-Mediated Bactericidal Activity of Human Antibodies to Poly 2->8 N-Acetylneuraminic Acid, the Capsular Polysaccharide of Neisseria meningitidis Serogroup B (1995)

Serum antibodies to Neisseria meningitidis group B (MenB) polysaccharide are reported not to elicit bacteriolysis in the presence of human complement. To reexamine this question, we evaluated the ability of two human IgM anti-MenB polysaccharide monoclonal antibodies (MAbs) and seven human MenB polysaccharide-reactive human IgM paraproteins to elicit bacteriolysis. In the presence of human complement, both MAbs and five of the seven paraproteins were bactericidal at antibody concentrations of 0.25-9.6 micrograms/mL (50% killing). Activity of the respective antibodies was enhanced 200- to > 10,000-fold when rabbit complement was used instead of human complement. With rabbit complement, the bactericidal activity of human IgM polyclonal antibody or MAb to Haemophilus influenzae type b (Hib) polysaccharide but not human IgG polyclonal antibody or MAb to Hib polysaccharide was similarly augmented. Thus, for both MenB and Hib, IgM antipolysaccharide antibodies elicit complement-mediated bactericidal activity in the presence of human complement, and the use of rabbit complement yields spuriously high activity.
Making Augmented Reality Work Outdoors Requires Hybrid Tracking (1999)

Developing Augmented Reality systems that work outdoors, rather than indoors in constrained environments, will open new application areas and motivate the construction of new, more general tracking approaches. Accurate tracking outdoors is difficult because we have little control over the environment and fewer resources available compared to an indoor application. This position paper examines the individual tracking technologies available and concludes that for the near term, a hybrid solution is the only viable approach. The distortion measured from an electronic compass and tilt sensor is discussed.
Differential privacy in telco big data platform (2015)

Differential privacy (DP) has been widely explored in academia recently but less so in industry possibly due to its strong privacy guarantee. This paper makes the first attempt to implement three basic DP architectures in the deployed telecommunication (telco) big data platform for data mining applications. We find that all DP architectures have less than 5% loss of prediction accuracy when the weak privacy guarantee is adopted (e.g., privacy budget parameter ε ≥ 3). However, when the strong privacy guarantee is assumed (e.g., privacy budget parameter ε ≤ 0:1), all DP architectures lead to 15% ~ 30% accuracy loss, which implies that real-word industrial data mining systems cannot work well under such a strong privacy guarantee recommended by previous research works. Among the three basic DP architectures, the Hybridized DM (Data Mining) and DB (Database) architecture performs the best because of its complicated privacy protection design for the specific data mining algorithm. Through extensive experiments on big data, we also observe that the accuracy loss increases by increasing the variety of features, but decreases by increasing the volume of training data. Therefore, to make DP practically usable in large-scale industrial systems, our observations suggest that we may explore three possible research directions in future: (1) Relaxing the privacy guarantee (e.g., increasing privacy budget ε) and studying its effectiveness on specific industrial applications; (2) Designing specific privacy scheme for specific data mining algorithms; and (3) Using large volume of data but with low variety for training the classification models.
Ideal anodization of silicon (1997)

Silicon has been anodized such that the porous layer is passivated with a homogeneous stretching phase by incorporating H2O2 in the anodization mixture. Fourier transform infrared spectroscopy measurements show that the Si–H stretching mode oriented perpendicular to the surface at ∼2100 cm−1 dominates the spectrum with negligible contribution from the bending modes in the 600–900 cm−1 region. Material analysis using Auger electron spectroscopy shows that the samples have very little impurities, and that the luminescent layer is very thin (5–10 nm). Scanning electron microscopy shows that the surface is smoother with features smaller than those of conventional samples.
Immune System Dysfunction and Autoimmune Disease in Mice Lacking Emk (Par-1) Protein Kinase (2001)

Emk is a serine/threonine protein kinase implicated in regulating polarity, cell cycle progression, and microtubule dynamics. To delineate the role of Emk in development and adult tissues, mice lacking Emk were generated by targeted gene disruption. Emk(-/-) mice displayed growth retardation and immune cell dysfunction. Although B- and T-cell development were normal, CD4(+)T cells lacking Emk exhibited a marked upregulation of the memory marker CD44/pgp-1 and produced more gamma interferon and interleukin-4 on stimulation through the T-cell receptor in vitro. In addition, B-cell responses to T-cell-dependent and -independent antigen challenge were altered in vivo. As Emk(-/-) animals aged, they developed splenomegaly, lymphadenopathy, membranoproliferative glomerulonephritis, and lymphocytic infiltrates in the lungs, parotid glands and kidneys. Taken together, these results demonstrate that the Emk protein kinase is essential for maintaining immune system homeostasis and that loss of Emk may contribute to autoimmune disease in mammals.
The Src-suppressed C kinase substrate, SSeCKS, is a potential metastasis inhibitor in prostate cancer. (2001)

The molecular mechanisms leading to prostate cancer remain poorly understood, especially concerning the progression to the metastatic form. SSeCKS, a major protein kinase C substrate with tumor suppressor activity, is likely the rodent orthologue of human Gravin/AKAP12, a scaffolding protein for protein kinases A and C. Gravin was mapped as a single-copy gene to 6q24-25.2, a hotspot for deletion in advanced prostate cancer, and therefore, we investigated the role of SSeCKS/Gravin in prostate oncogenesis. SSeCKS/Gravin protein was detected in untransformed rat and human prostate epithelial cell lines EP12 and PZ-HPV-7, respectively, and in human prostatic epithelium, especially basal epithelial cells. In contrast, SSeCKS/Gravin protein and RNA levels were severely reduced in human (PC-3, PPC-1, LNCaP, DU145, and TSU) and rat Dunning (AT3.1 and MatLyLu) prostate cancer cell lines. The regulated reexpression of SSeCKS in MatLyLu cells induced filopodia-like projections and a decrease in anchorage-independent growth. In nude mice, SSeCKS reexpression slightly decreased primary-site tumor growth but severely decreased the formation of lung metastases. Primary-site tumors that progressed lost regulated SSeCKS reexpression. SSeCKS/Gravin expression was detected in benign human prostatic lesions and well-differentiated carcinomas but not in undifferentiated lesions with Gleason sums > or =6. Our data suggest a role for the loss of SSeCKS/Gravin in the metastatic progression of human prostate cancer.
Participation of Periodontal Ligament Cells With Regeneration of Alveolar Bone (2001)

DPLC retain the capability to differentiate into an osteoblast lineage and may act in the regeneration of periodontal ligament with new cementum formation, whereas these cells may have a limited influence on alveolar bone formation during the course of periodontal regeneration.
Ku Heterodimer-Independent End Joining inTrypanosoma bruceiCell Extracts Relies upon Sequence Microhomology (2007)

DNA double-strand breaks (DSBs) are repaired primarily by two distinct pathways: homologous recombination and nonhomologous end joining (NHEJ). NHEJ has been found in all eukaryotes examined to date and has been described recently for some bacterial species, illustrating its ancestry. Trypanosoma brucei is a divergent eukaryotic protist that evades host immunity by antigenic variation, a process in which homologous recombination plays a crucial function. While homologous recombination has been examined in some detail in T. brucei, little work has been done to examine what other DSB repair pathways the parasite utilizes. Here we show that T. brucei cell extracts support the end joining of linear DNA molecules. These reactions are independent of the Ku heterodimer, indicating that they are distinct from NHEJ, and are guided by sequence microhomology. We also demonstrate bioinformatically that T. brucei, in common with other kinetoplastids, does not encode recognizable homologues of DNA ligase IV or XRCC4, suggesting that NHEJ is either absent or mechanistically diverged in these pathogens.
Análisis e identificación de bioestimulantes indólicos en una composta. (2005)

The production of compost is one of the alternatives for the disposal of non-hazardous solid wastes. Compost is used in agriculture and gardening as fertilizer. Samples for commercial compost were used to evaluate biological activity. The extract from compost was done using organic solvents and shaking the sample for about 24 hours under relatively low temperature (2-4 oC). The purification was made using Adsorbex LiChrolut RP-18 column packed with synthetic silica gel. The bioassays play an important role in the identification of subtances actives in compost. The bioassays consisted in the root growth test of cress (Lepidium sativum), amaranto (Amaranthus hybridus) and wheat (Triticum aestivium). Three replicates of each sample were analyzed in each one the four bioassays. The FT-infrared spectrum of extract compost in the region 4400-450 cm-1 was measured on a Perkin Elmer 1600 spectrometer. Bioassay demostrates the presence of compound with biological activity, in our analysis was corroborated. We can conclude therefore, that there is sufficient evidence of a compound with biological activity in the analyzed sample of the compost which is similar to indol acetic acid