gebhart/patrepeval huggingface dataset:
DeSUMOylating enzymes—SENPs (2008)

Modification of proteins by ubiquitin and SUMO (small ubiquitin-like modifiers) is a dynamic and reversible process. Similar to the ubiquitin pathway, where the action of deubiquitinating enzymes removes ubiquitin from ubiquitin-adducts, SUMO is also removed intact from its substrates by proteases belonging to the sentrin-specific proteases (SENPs) family. In addition to their isopeptidase activity, SENPs also execute another essential function as endopeptidases by removing the short C-terminal extension from immature SUMOs. The defining characteristics of SENPs are their predicted conserved molecular scaffold-defined as members of peptidase Clan CE, conserved catalytic mechanism, and their reported activity on SUMO or Nedd8 conjugated proteins (or the respective precursors). We discuss recent progress on the human SENPs and their substrates.
Defective proliferative capacity and accelerated telomeric loss of hematopoietic progenitor cells in rheumatoid arthritis (2008)

In RA, circulating bone marrow-derived progenitor cells were diminished, and concentrations stagnated at levels typical of those in old control subjects. HPCs from RA patients displayed growth factor nonresponsiveness and sluggish cell cycle progression; marked telomere shortening indicated proliferative stress-induced senescence. Defective HPC function independent of disease activity markers suggests bone marrow failure as a potential pathogenic factor in RA.
Droplet-based microfluidics in drug discovery, transcriptomics and high-throughput molecular genetics (2016)

Droplet-based microfluidics enables assays to be carried out at very high throughput (up to thousands of samples per second) and enables researchers to work with very limited material, such as primary cells, patient's biopsies or expensive reagents. An additional strength of the technology is the possibility to perform large-scale genotypic or phenotypic screens at the single-cell level. Here we critically review the latest developments in antibody screening, drug discovery and highly multiplexed genomic applications such as targeted genetic workflows, single-cell RNAseq and single-cell ChIPseq. Starting with a comprehensive introduction for non-experts, we pinpoint current limitations, analyze how they might be overcome and give an outlook on exciting future applications.
Characteristics of Hook Formation by Bean Seedlings (1972)

Explants were isolated from 6-day-old etiolated bean seedlings (Phaseolus vulgaris L. cv. Black Valentine) containing the cotyledons with 4 mm of hypocotyl just below the node and/or the epicotyl. During incubation on distilled water, uneven growth of the hypocotyl or epicotyl occurred resulting in the formation of a hook. The more rapid growth of the side which became convex was not dependent upon the presence of the slower growing concave side. It was concluded that the main axis has an intrinsic capacity for asymmetric growth. The growth leading to hook formation was inhibited by alpha-naphthaleneacetic acid at concentrations above 0.2 milligram per liter.
p50 Nuclear Factor-κB Overexpression in Tumor-Associated Macrophages Inhibits M1 Inflammatory Responses and Antitumor Resistance (2006)

Tumor-associated macrophages (TAM) are a major inflammatory infiltrate in tumors and a major component of the protumor function of inflammation. TAM in established tumors generally have an M2 phenotype with defective production of interleukin-12 (IL-12) and high IL-10. Here, we report that defective responsiveness of TAM from a murine fibrosarcoma and human ovarian carcinoma to M1 activation signals was associated with a massive nuclear localization of the p50 nuclear factor-kappaB (NF-kappaB) inhibitory homodimer. p50 overexpression inhibited IL-12 expression in normal macrophages. TAM isolated from p50(-/-) mice showed normal production of M1 cytokines, associated with reduced growth of transplanted tumors. Bone marrow chimeras showed that p50 inactivation in hematopoietic cells was sufficient to result in reduced tumor growth. Thus, p50 NF-kappaB overexpression accounts for the inability of TAM to mount an effective M1 antitumor response capable of inhibiting tumor growth.
Three-Dimensional Lookup Table with Interpolation (2010)

Color space transformation using a 3D lookup table (LUT) with interpolation is used to correlate the source and destination color values in the lattice points of a 3D table, where nonlattice points are interpolated by using the nearest lattice points. This method has been used in many applications with quite satisfactory results, and incorporated into the ICC profile standard. In this chapter, the structure of the 3D-LUT approach is discussed and the mathematical formulations of interpolation methods are given. These methods are tested using several sets of data points. The similarities and differences of these interpolation methods are discussed.
KIT oncogene inhibition drives intratumoral macrophage M2 polarization (2013)

Tumor-associated macrophages (TAMs) are a major component of the cancer microenvironment. Modulation of TAMs is under intense investigation because they are thought to be nearly always of the M2 subtype, which supports tumor growth. Gastrointestinal stromal tumor (GIST) is the most common human sarcoma and typically results from an activating mutation in the KIT oncogene. Using a spontaneous mouse model of GIST and 57 freshly procured human GISTs, we discovered that TAMs displayed an M1-like phenotype and function at baseline. In both mice and humans, the KIT oncoprotein inhibitor imatinib polarized TAMs to become M2-like, a process which involved TAM interaction with apoptotic tumor cells leading to the induction of CCAAT/enhancer binding protein (C/EBP) transcription factors. In human GISTs that eventually developed resistance to imatinib, TAMs reverted to an M1-like phenotype and had a similar gene expression profile as TAMs from untreated human GISTs. Therefore, TAM polarization depends on tumor cell oncogene activity and has important implications for immunotherapeutic strategies in human cancers.
druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico (2017)

Deep generative adversarial networks (GANs) are the emerging technology in drug discovery and biomarker development. In our recent work, we demonstrated a proof-of-concept of implementing deep generative adversarial autoencoder (AAE) to identify new molecular fingerprints with predefined anticancer properties. Another popular generative model is the variational autoencoder (VAE), which is based on deep neural architectures. In this work, we developed an advanced AAE model for molecular feature extraction problems, and demonstrated its advantages compared to VAE in terms of (a) adjustability in generating molecular fingerprints; (b) capacity of processing very large molecular data sets; and (c) efficiency in unsupervised pretraining for regression model. Our results suggest that the proposed AAE model significantly enhances the capacity and efficiency of development of the new molecules with specific anticancer properties using the deep generative models.
PLRS - JTIDS Hybrid (PJH) Satellite Overlay Concept (1984)

This paper will define the system architecture and explore the benefits of the PJH synchronous TDMA (Time Domain Multiple Access) communications system overlaid by satellite communications links. The composite system in its ultimate configuration can feature real-time control of the satellite/PJH linkages and provide a synergistic, non-monolithic combined communications system with selective high-capacity links. Also, inherent PJH battle damage resistance and optimal relaying can be enhanced with the satellite overlay. Obviously, where applicable, the position location and Identification Friend, Foe or Neutral (IFFN) capabilities can be retained. Overall, the secure jam-resistant, weather independency of PJH will enhance point-to-point satellite system reliability, particularly when EHF tactical satellite systems are employed.
Regulation of gene expression, cellular localization, and in vivo function of Caenorhabditis elegans DNA topoisomerase I (2001)

These phenotypes, along with expressional regulations, demonstrate that DNA topoisomerase I plays important roles in rapidly growing germ cells and embryonic cells.
Re-evaluation of the 3 alpha-hydroxysteroid dehydrogenase assay for total bile acids in bile. (1978)

A review of the 3 alpha-hydroxysteroid dehydrogenase method for determining the concentration of total bile acids in bile is described. The optimum conditions for the assay were established with respect to pH, temperature, incubation time, amount of NAD+, and units of enzyme activity required to obtain complete oxidation of the substrate under fixed conditions. Furthermore, the effect of hydrazine hydrate, methanol, and bile volume on the reaction was examined. It was also established that the bile acid concentration in bile samples with a high molar percentage of cholesterol would be overestimated if 3 beta-hydroxysteroid dehydrogenase were present with the 3 alpha-enzyme.
Comparison of Urinary Bladder Function in Rats with Hereditary Diabetes Insipidus, Streptozotocin-Induced Diabetes Mellitus, and Nondiabetic Osmotic Diuresis (1994)

In vivo and in vitro bladder function were studied in three different models of increased diuresis: 1) Brattleboro rats with hereditary diabetes insipidus (di/di), 2) Sprague-Dawley rats with streptozotocin-induced diabetes mellitus (STZ), and 3) Sprague-Dawley rats with increased diuresis due to 5% sucrose added to the drinking water. When compared with controls, all three models showed bladder mass, increased water consumption and urine output, higher mean and maximal increased micturition volumes, and greater bladder capacity and compliance by in vitro cystometry. The changes were more extensive in di/di rats than in the STZ and sucrose-drinking rats. The concentration of bladder collagen decreased in all three rat models when compared with controls. However, the collagen concentration of STZ bladders was significantly lower than the collagen concentration of di/di and sucrose bladders, suggesting that the decrease in bladder collagen concentration associated with experimental diabetes mellitus is only partly related to the increased diuresis. Contractile function was studied using a whole bladder model. Responses of whole bladders from control and diabetic rats to electrical field stimulation, carbachol and KCl were identical. Volume-pressure relations of the isolated whole bladder showed that the magnitude of the contractile response to KCl is constant at intravesical volumes ranging from about 10 to 95% of cytometrical bladder capacity. Bladders from Brattleboro di/di rats and STZ rats showed a rightward shift of volume-passive pressure curves when compared with appropriate controls. Bladders from sucrose-drinking rats had volume-passive pressure curves similar to the bladders from controls. This study suggests that while contractile function remains intact with increased diuresis, the passive function changes, with the bladder becoming more distensible.
Ebola Virus Does Not Induce Stress Granule Formation during Infection and Sequesters Stress Granule Proteins within Viral Inclusions (2016)

Although progress has been made developing antiviral therapeutics and vaccines against the highly pathogenic Ebola virus (EBOV), the cellular mechanisms involved in EBOV infection are still largely unknown. To better understand these intracellular events, we investigated the cellular stress response, an antiviral pathway manipulated by many viruses. We show that EBOV does not induce formation of stress granules (SGs) in infected cells and is therefore unrestricted by their concomitant translational arrest. We identified SG proteins sequestered within viral inclusions, which did not impair protein translation. We further show that EBOV is unable to block SG formation triggered by exogenous stress early in infection. These findings provide insight into potential targets of therapeutic intervention. Additionally, we identified a novel function of the interferon antagonist VP35, which is able to disrupt SG formation.
Prevention of HLA immunization with leukocyte-poor packed red cells and platelet concentrates obtained by filtration (1988)

HLA immunization is a common complication of transfusion therapy in 30% to 60% of oncohematologic patients. Evidence shows that leukocytes present in cellular blood products are the main component involved in the occurrence of HLA immunization, and several studies showed that leukocyte-poor blood products are less able to induce it. However, leukocyte-poor platelet concentrates obtained by conventional techniques, ie, centrifugation, frequently have a high level of remaining leukocytes. Cotton wool filter Imugard IG 500 can be used to obtain leukocyte-poor cellular blood products. The technique is easy to perform, even in an emergency, and can be used with either packed RBCs or platelet concentrates. Means of 97%, 92%, and 76% elimination of leukocytes are obtained for packed RBCs, pooled standard platelet concentrates, and single-donor platelet concentrates, respectively. Patients were randomized to receive either standard (control group) or filtered (leukocyte-poor group) blood products. Of 112 randomized patients, 69 were evaluable, 35 in the control group and 34 in the leukocyte-poor group. Both groups are comparable according to age, diagnosis, sex ratio, previous transfusions, and pregnancies. There is a significant difference in regard to the HLA immunization rate (31.4% in the control v 11.7% in the leukocyte-poor group, P less than .05) and frequency of refractoriness to platelet transfusions (46.6% v 11.7%, P less than .05). We conclude that this filtration technique can be an efficient means to reduce the HLA immunization rate in polytransfused oncohematologic patients.
A generalization to the Teager-Kaiser energy function and application to resolving two closely-spaced tones (2002)

Based on physical considerations, Kaiser (1990) proposed a new energy function for discrete time signals, known as the Teager-Kaiser energy function (TKEF). An interesting property of the TKEF is that if the input signal consists of two closely-spaced tones (amplitude modulated signal), the TKEF produces the difference frequency tone (envelope signal). However, a drawback is that the TKEF is highly sensitive to additive noise. We propose a generalized TKEF (GTKEF) to reduce the noise sensitivity. Fortunately, it turns out that the generalization can be used to enhance the sum frequency tone as well. This enables us to apply the GTKEF to resolve of two closely-spaced tones. The result can be viewed as an interesting nonlinear preprocessing scheme that can be used to transform a signal consisting of two closeby frequencies at f/sub 1/ and f/sub 2/ into a signal consisting of frequencies at (f/sub 1/-f/sub 2/) and (f/sub 1/+f/sub 2/). Clearly, it is much easier to resolve the latter frequencies, whichever spectral analysis method is used.
Enhancement of testosterone secretion by normal adult human Leydig cells by co‐culture with enriched preparations of normal adult human Sertoli cells (1993)

An in-vitro method was developed to study Sertoli-Leydig cell interactions in man, using testes removed at the time kidneys were removed for transplantation from 6 young adult men (aged 17-45 years) after cerebral death. After collagenase digestion of testicular tissue, Leydig cells were purified on discontinuous Percoll gradients. Two fractions of Leydig cells, 'L2' and 'L3' which differed in their buoyant density (1.05 g < L2 < 1.06 g and 1.06 g < L3 < 1.08 g), were obtained. The Sertoli cell-enriched preparation was obtained from seminiferous tubular fragments after sequential treatment with glycine buffer to remove peritubular-myoid cells, a second collagenase digestion, mechanical fragmentation and washes to remove germ cells. Purified Leydig cells were then cultured either alone or together with Sertoli cells in culture dishes coated with collagen, fibronectin and laminin in a chemically defined medium without serum. The influence of co-culture on basal testosterone secretion was examined in 3 successive 48 h periods.(ABSTRACT TRUNCATED AT 250 WORDS)
Novel cage compounds from inter-intra-molecular Diels–Alder reactions of 1,2,4-triazines with cyclo-octa-1,5-diene (1988)

1,2,4-Triazines with electron-withdrawing substituents at the three position react with cyclo-octa-1,5-diene by intermolecular Diels–Alder addition followed by elimination of nitrogen; the 2-azadiene so formed then undergoes an intramolecular Diels–Alder reaction producing novel cage compounds.
The Enzymic Interconversion of Acetate and Acetyl-coenzyme A in Escherichia coli (1977)

Mutants of Escherichia coli K12 have been isolated that grow on media containing pyruvate of proline as sole carbon sources despite the presence of 10 or 50 mM-sodium fluoroacetate. Such mutants lack either acetate kinase [ATP: acetate phosphotransferase; EC 2.7.2.1] or phosphotransacetylase [acetyl-CoA: orthophosphate acetyltransferase; EC 2.3.1.8] activity. Unlike wild-type E. coli, phosphotransacetylase mutants do not excrete acetate when growing aerobically or anaerobically on glucose; their anaerobic growth on this sugar is slow. The genes that specify acetate kinase (ack) and phosphotransacetylase (pta) activities are cotransducible with each other and with purF and are thus located at about min 50 on the E. coli linkage map. Although Pta- and Ack- mutants are greatly impaired in their growth on acetate, they incorporate [2-14C]acetate added to cultures growing on glycerol, but not on glucose. An inducible acetyl-CoA synthetase [acetate: CoA ligase (AMP-forming); EC 6.2.1.1] effects this uptake of acetate.
Effects of supplementation with branched chain amino acids and ornithine aspartate on plasma ammonia and central fatigue during exercise in healthy men (2015)

Supplementation with BCAA and OA is a useful way to improve MCRT during high-intensity exercise and accelerate the elimination of ammonia at the recovery stage after exercise in healthy young men.
Cathepsin D in the malignant progression of neoplastic diseases (review). (1992)

Recent studies suggest that aspartic proteinase Cathepsin D may be implicated in the process of tumor invasion and metastasis. In fact several in vitro observations showed that this proteinase may facilitate the spread of neoplastic cells through different mechanisms related to its proteolytic activity, by acting at different levels of the metastatic cascade. Cathepsin D may promote tumor cell proliferation by acting as an autocrine mitogen through the activation of latent forms of growth factors or by interacting with growth factor receptors. The enzyme was also shown to be able to degrade in vitro extracellular matrix and to activate latent precursors forms of other proteinases involved in the invasive steps of the metastatic process. Although unequivocal proof of its active role in promoting these processes also in vivo has not been obtained so far, recent clinical observations which showed a positive correlation between levels of expression of Cathepsin D activity and malignant progression of some human neoplasms further support this hypothesis. These findings warrant extensive experimental and clinical studies to better assess the pathophysiological role of this acid proteinase in the spread of neoplastic diseases and suggest new and more selective therapeutic approaches to the treatment of human neoplasms.
Analyzing Development of Group Cognition (2015)

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"Präsidentschaftswahl" in Belarus: autoritäres Regime, abhängige Staatswirtschaft, internationale Isolation (2006)

'Belarus ist ein ebenso wichtiger wie problematischer Nachbarstaat der EU. In diesem Land werden derzeit die autoritären Machtstrukturen dramatisch ausgeweitet. Die manipulierte Präsidentschaftswahl und der massive Gewalteinsatz gegen friedliche Demonstranten haben den Charakter der Minsker Herrschaft verdeutlicht. Ausgehend von den Wahlen am 19. März 2006 und dem anschließenden Protest der Opposition, erläutert die Studie die vier zentralen Säulen, auf denen das Machtsystem von Präsident Alexander Lukaschenko beruht: das sowjetische Erbe, die autoritäre Herrschaft, die abhängige Staatswirtschaft und die internationale Abschottung. Darüber hinaus wird die Frage nach Stabilität oder Fragilität der Herrschaft angesichts der abhängigen Wirtschaft, wachsender innerer Widersprüche und internationaler Selbstisolierung Belarus' gestellt. Die maßgebenden europäischen und amerikanischen Akteure haben sich Anfang 2006 auf gemeinsame politische Schritte gegenüber Belarus verständigt. Nachdem Washington und Brüssel in der Vergangenheit in den Beziehungen mit dem EU-Nachbarn Belarus unterschiedliche Strategien verfolgt hatten, hat der Druck des vom Regime überstürzt angesetzten Urnengangs USA und EU zu konzertiertem Handeln veranlasst. Neben einer Politik der ausgestreckten Hand gegenüber dem Staat Belarus und seinen Einwohnern sind die EU und USA entschlossen, die Wahlergebnisse gemeinsam zu bewerten und abgestimmt auf sie zu reagieren.' (Autorenreferat)
Electron mobility exceeding 104 cm2/V s in an AlGaN–GaN heterostructure grown on a sapphire substrate (1999)

High-quality AlGaN/GaN undoped single heterostructures (SH) with different Al contents have been grown on sapphire substrates. The magnetotransport investigation was performed on these samples at a low temperature. The observation of Shubnikov–de Hass oscillations in the magnetic fields below 3 T and the integer quantum Hall effect confirmed the existence of the two-dimensional electron gas (2DEG) at the AlGaN/GaN interface. The Al0.18Ga0.82N/GaN SH shows a Hall mobility of 10 300 cm2/V s at a carrier sheet density of 6.19×1012/cm2 measured at 1.5 K. To the best of our knowledge, this is the highest carrier mobility ever measured in GaN-based semiconductors grown on sapphire substrates. The Al composition dependence of the mobility and carrier sheet density were also investigated. Based on the piezoelectric field effect, the Al composition dependence of the 2DEG sheet density was calculated, which agreed well with the experimental result. The negative magnetoresistance with parabolic magnetic-field dependence in the low magnetic field was also observed in the sample with the highest 2DEG sheet density.
Effect of Resynchronization Therapy Stimulation Site on the Systolic Function of Heart Failure Patients (2001)

CRT with LV free wall stimulation produced significantly better LV systolic performance compared with anterior stimulation. Further studies are warranted to prove the clinical superiority of the LV free wall as a site for long-term CRT.