gebhart/patrepeval huggingface dataset:
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes (2016)

The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
Immunologic and clinical effects of antibody blockade of cytotoxic T lymphocyte-associated antigen 4 in previously vaccinated cancer patients (2008)

Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) functions as a negative regulator of endogenous and vaccine-induced antitumor immunity. The administration of fully human anti-CTLA-4 blocking monoclonal antibodies to advanced-cancer patients increases immune-mediated tumor destruction in some subjects. Nonetheless, patients that respond also frequently manifest serious inflammatory pathologies, raising the possibility that the therapeutic and toxic effects of CTLA-4 blockade might be linked. Here we show that periodic infusions of anti-CTLA-4 antibodies after vaccination with irradiated, autologous tumor cells engineered to secrete GM-CSF (GVAX) generate clinically meaningful antitumor immunity without grade 3 or 4 toxicity in a majority of metastatic melanoma patients. The application of this sequential immunotherapy to advanced ovarian carcinoma patients also revealed that tumor destruction and severe inflammatory pathology could be dissociated, although further refinements are required to increase clinical responses and to minimize toxicity in this population. The extent of therapy-induced tumor necrosis was linearly related to the natural logarithm of the ratio of intratumoral CD8(+) effector T cells to FoxP3(+) regulatory T cells (Tregs) in posttreatment biopsies. Together, these findings help clarify the immunologic and clinical effects of CTLA-4 antibody blockade in previously vaccinated patients and raise the possibility that selective targeting of antitumor Tregs may constitute a complementary strategy for combination therapy.
Hepatic lipocytes: the principal collagen-producing cells of normal rat liver. (1985)

Hepatic lipocytes were isolated from normal rat liver and established in culture. A virtually pure isolate was obtained by fractionating enzymatically digested liver on a discontinuous gradient of arabinogalactan. Isolated cells displayed prominent rough endoplasmic reticulum and typical cytoplasmic droplets containing vitamin A. Lipocytes in primary culture were shown by immunofluorescence to secrete collagen types I, III, and IV and also laminin. Immunoassay of culture media showed that lipocytes during the first week in culture secrete type I (72.1-86.2% of total measured soluble collagen), type III (2.6-7.2%), and type IV (11.2-29.7%) collagens. Five percent of total secreted protein was collagen compared with 0.2% in similarly cultured hepatocytes and 1.7% in sinusoidal endothelial cells, as measured by the production of peptide-bound [3H]hydroxyproline in cells incubated with [3H]proline. The calculated amount of collagen synthesized by lipocytes per microgram of cellular DNA was 10-fold greater than that produced by hepatocytes and over 20-fold greater than that produced by endothelial cells. The findings indicate that collagen synthesis and secretion are specialized functions of hepatic lipocytes, and that, in cells from normal liver, this represents production primarily of type I collagen. The phenotypic resemblance of these cells to fibroblasts supports the hypothesis that lipocytes are a major source of collagen in pathologic fibrosis and may be precursors of the fibroblast-like cells observed in liver injury.
ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB (2013)

Transposable elements belonging to the recently identified IS200/IS605 family radically differ from classical insertion sequences in their transposition mechanism by strictly requiring single-stranded DNA substrates. This IS family includes elements encoding only the transposase (TnpA), and others, like ISDra2 from Deinococcus radiodurans, which contain a second gene, tnpB, dispensable for transposition and of unknown function to date. Here, we show that TnpB has an inhibitory effect on the excision and insertion steps of ISDra2 transposition. This inhibitory action of TnpB was maintained when ISDra2 transposition was induced by γ-irradiation of the host cells and required the integrity of its putative zinc finger motif. We also demonstrate the negative role of TnpB when ISDra2 transposition was monitored in a heterologous Escherichia coli host, indicating that TnpB-mediated inhibition does not involve Deinococcus-specific factors. TnpB therefore appears to play a regulatory role in ISDra2 transposition.
Chemokine Receptors in Human Endothelial Cells (1998)

Chemokines play an important role in the regulation of endothelial cell (EC) function, including proliferation, migration and differentiation during angiogenesis, and re-endothelialization after injury. In this study, reverse transcriptase-polymerase chain reaction was used to reveal expression of various CXC and CC chemokine receptors in human umbilical vein EC. Northern analysis showed that CXCR4 was selectively expressed in vascular EC, but not in smooth muscle cells. Compared with other chemokines, stromal cell-derived factor-1alpha (SDF-1alpha), the known CXCR4 ligand, was an efficacious chemoattractant for EC, causing the migration of approximately 40% input cells with an EC50 of 10-20 nM. Of the chemokines tested, only SDF-1alpha induced a rapid, though variable mobilization of intracellular Ca2+ in EC. Experiments with actinomycin D demonstrated that CXCR4 transcripts were short-lived, indicating a rapid mRNA turnover. Interferon-gamma (IFN-gamma) caused a pronounced down-regulation of CXCR4 mRNA in a concentration- and time-dependent manner. In a striking functional correlation, IFN-gamma treatment also attenuated the chemotactic response of EC to SDF-1alpha. IL-1beta, tumor necrosis factor-alpha, and lipopolysaccharide produced a time course-dependent biphasic effect on CXCR4 transcription. Expression of CXCR4 in EC is significant, more so as it and several CC chemokine receptors have been shown to serve as fusion co-receptors along with CD4 during human immunodeficiency virus infection. Taken together, these findings provide evidence of chemokine receptor expression in EC and offer an explanation for the action of chemokines like SDF-1alpha on the vascular endothelium.
A Model-Aided Segmentation in Urethra Identification Based on an Atlas Human Autopsy Image for Intensity Modulated Radiation Therapy (2007)

In order to protect urethra in radiation therapy of prostate cancer, the urethra must be identified and localized as an organ at risk (OAR) for the inverse treatment planning in intensity modulated radiation therapy (IMRT). Because the prostatic urethra and its surrounding prostate tissue have similar physical characteristics, such as linear attenuation coefficient and density, it is difficult to distinct the OAR from the target in CT images. To localize the urethra without using contrast agent or additional imaging modalities other than planning CT images, a different approach was developed using a standard atlas of human anatomy image. This paper reports an investigation, in which an adult urethra was modeled based on a human anatomic image. An elastic model was build to account for a uniform tissue deformation of the prostate. This model was then applied to patients to localize their urethras and preliminary results are presented.
Size, laminar and columnar distribution of efferent cells in the sensory‐motor cortex of monkeys (1977)

Abstract The cells of origin of cortico‐cortical and subcortical projections from the subfields of the somatic sensory area and from the motor cortex have been identified in cynomolgus and squirrel monkeys by the retrograde axonal transport method. The somata of the cells of origin of a particular fiber system have a specific laminar or sublaminar distribution. The somata of the majority of cortico‐cortical cells lie in the supragranular layers. Those projecting to the opposite cortex are confined to the deeper half of layer III (layer IIIB). Ipsilateral cortico‐cortical neurons lie mainly superficial to them in layers IIIA and II, but in the second somatic sensory area (SII) and in area 2 of the first (SI), small numbers are also found in layer V. Corticospinal cells lie in the deeper part of layer V and corticostriatal cells in the superficial part. Corticopontine, corticobulbar and corticorubral cells lie in between. The majority of corticothalamic cells lies in layer VI but a second, smaller population is found in the deep part of layer V. The cells giving rise to a particular set of efferent connections can be distinguished in terms of size and, with the exception of the corticospinal cells, their size does not vary greatly from area to area. In many cases, the size and laminar specificity indicates that cells sending axons to one site cannot have collateral branches projecting to another. In most of the fiber systems studied, labeled cells form single or multiple strips, 0.5–1 mm wide and oriented mediolaterally across the cortex. The strips appear in all of the subfields of the somatic sensory and motor areas and may form the basis of the clustering of like groups of efferent neurons demonstrable in physiological studies.
Matrix-independent Survival of Human Keratinocytes through an EGF Receptor/MAPK-Kinase-dependent Pathway (2001)

Normal epithelial cells undergo apoptosis when they are denied contact with the extracellular matrix, in a process termed "anoikis." Conversely, malignant epithelial cells typically acquire anchorage independence, i.e., the capacity to survive and grow in the absence of matrix interaction. Here we asked the question whether anoikis is affected by signaling through the EGF receptor (EGFR). We focused on the EGFR because EGFR signaling is frequently deregulated in malignant epithelial cells. We demonstrate that EGFR activation markedly alleviated the requirement of matrix engagement for survival of primary and immortalized human keratinocytes in suspension culture. Protection of epithelial cells through EGFR activation against anoikis was associated with and required sustained MAPK phosphorylation during the early phase of suspension culture. Interestingly, high levels of MAPK phosphorylation were not only required for EGFR-mediated protection against anoikis but also occurred as a consequence of caspase activation at later stages of suspension culture. These results demonstrate that EGFR activation contributes to anchorage-independent epithelial cell survival and identify MAPK activation as an important mechanism in this process.
A Comparison of Corneal Autografts With Homografts (1998)

* BACKGROUND AND OBJECTIVE: To determine whether ensured graft acceptance through the use of corneal autografts yields a better outcome than when standard homografts are used. * PATIENTS AND METHODS: Four patients who needed a corneal transplant in one eye and who had a blind fellow eye underwent a corneal autograft in the eye with corneal pathology. * RESULTS: Three of the four patients had clear grafts on long-term follow-up, and no patient experienced immunologic graft rejection. However, two of the four patients had large amounts of astigmatism postoperatively. * CONCLUSION: Autografts provided protection against immunologic graft rejection. However, because corneal autografts yielded unpredictable amounts of astigmatism, their outcomes are not necessarily better than those of homografts. [Ophthalmic Surg Lasers 1998;29:305-308.]
The relationship between attractive interparticle forces and bulk behaviour in dry and uncharged fine powders (2005)

Memento, homo, qui pulvis est et pulverem reverteris. Genesis 3 Polvos serán, mas polvo enamorado. Francisco de Quevedo The physics of granular materials in ambient gases is governed by interparticle forces, gas–particle interaction, geometry of particle positions and geometry of particle contacts. At low consolidations these are strongly dependent on the external forces, boundary conditions and on the assembling procedure. For dry fine powders of micron and sub-micron particle size interparticle attractive forces are typically much higher than particle weight, and particles tend to aggregate. Because of this, cohesive powders fracture before breaking, flow and avalanche in coherent blocks much larger than the particle size. Similarly the drag force for micron sized particles is large compared to their weight for velocities as low as 1 mm/s. Due to this extreme sensitivity to interstitial gas flow, powders transit directly from plastic dense flows to fluidization without passing through collisional regimes with negligible gas interaction. These two features, strong attractive forces and strong gas interaction make powder behaviour differ qualitatively from the behaviour of large, noncohesive grains. In this paper we investigate the implications of these two features on the bulk powder behaviour. More in particular, the aim of this paper is to examine the relationship between attractive interparticle forces at grain level, with solid bulk properties at low consolidations (solid fraction, stresses), fluidization (aggregation, settling) and flow regime boundaries (plastic flow, inertial flow, fluidization and suspension). Many of the experimental results reported here are for dry and uncharged fine powders made of polymer particles of the order of 10 microns in diameter. However, the basic concepts and methodology are of general applicability. The relationship between attractive interparticle forces and bulk behaviour in dry and uncharged fine powdersAll authorsA. Castellanoshttps://doi.org/10.1080/17461390500402657Published online:19 February 2007Table Download CSVDisplay Table
Differential Cerebral Metabolic Changes With Paroxetine Treatment of Obsessive-Compulsive Disorder vs Major Depression (2002)

Brain metabolic responses to SRIs are both disorder-specific and response-specific. They vary according to the underlying pathophysiology of the patient and the degree of symptomatic improvement.
Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. (1995)

Each of four possible sets of mismatches (G.A/C.T, C.C/G.G, A.A/T.T, and C.A/G.T) containing the 8 possible single-base-pair mismatches derived from isolated mutations were examined to test the ability of T4 endonuclease VII to consistently detect mismatches in heteroduplexes. At least two examples of each set of mismatches were studied for cleavage in the complementary pairs of heteroduplexes formed between normal and mutant DNA. Four deletion mutations were also included in this study. The various PCR-derived products used in the formation of heteroduplexes ranged from 133 to 1502 bp. At least one example of each set showed cleavage of at least one strand containing a mismatch. Cleavage of at least one strand of the pairs of heteroduplexes occurred in 17 of the 18 known single-base-pair mutations tested, with an A.A/T.T set not being cleaved in any mismatched strand. We propose that this method may be effective in detecting and positioning almost all mutational changes when DNA is screened for mutations.
Neurochemical Studies of Early-Onset Alzheimer's Disease (1985)

Multiple neurotransmitter deficits found in recent autopsy studies of patients with Alzheimer's disease may militate against the success of "simple cholinergic replacement" as treatment. To study acetylcholine synthesis, we measured the incorporation of radiolabeled glucose into the transmitter in temporal-cortex specimens obtained at diagnostic craniotomy in 17 young patients with Alzheimer's disease. Synthesis of acetylcholine was significantly correlated with cognitive impairment. These results are consistent with the view that the deficit in the presynaptic cholinergic system is a relatively early change in the development of the clinical features of the disease. Other alterations in noradrenergic cells, some cortical neurons, postsynaptic cortical receptors, and possibly serotoninergic cells may not be closely associated with Alzheimer's disease.
Single amino acid insertions probe the alpha subunit of the Escherichia coli F1F0-ATP synthase. (1994)

Single amino acid insertions of alanine or aspartate have been introduced into the alpha subunit of the F1F0-ATP synthase at seven different sites, after residues 187, 193, 198, 202, 212, 217, and 222. These sites span a highly conserved region of the alpha subunit, parts of which are thought to be located in transmembrane spanning regions. Alanine insertions have little or no effect on function after positions 187, 193, 198, and 202, indicating that the region spanned by these residues is not essential for function. Alanine insertions after residues 212 and 217 disrupt ATP synthase function without grossly affecting the assembly of the enzyme, while the alanine insertion after residue 222 disrupts both ATP synthase function and assembly. All of the aspartate insertions are deleterious to ATP synthase function, except after residue 198. At the other six sites, aspartate insertions prevent growth on succinate minimal medium, indicating an inability to synthesize ATP. Aspartate insertions after residues 187 and 193 result in alpha subunits that do not fractionate with membranes, as indicated by immunoblotting. These results support a model of the alpha subunit in which residues 187-193 and residues 212-222 are part of distinct transmembrane spans, separated by a short extramembrane loop. The results are consistent with an important interaction between residues 212-222 of the alpha subunit and b or c subunits. General aspects of "insertion scanning mutagenesis" are also discussed.
조계종 전통의 창조와 혼종적 근대성: 서구 근대불교와의 비교를 중심으로 (2016)

한국 근대불교의 성격을 파악하기 위해서는 근대불교 보편의 요소와 함께 한국 적 특수성을 이해해야 하며, 식민지 국가로서의 조건 역시 고려해야 한다. 1941년 `조선 불교조계종`이 수립하고자 했던 한국불교의 전통은 문자 그대로 `과거에 존재했던 역사의 재현`이 아니라 근대의 관점에서 이상화되고 재구성된 `창조된 전통`이라고 볼 수 있다. 호미 바바의 개념을 빌려온다면 이 전통은 근대와 전근대, 탈근대의 혼종성(混種性, hybridity)을 지닌다. `혼종성`은 본질주의적 문화이해 및 이에 근거한 이분법을 극복하고자 고안된 개념이다. `근대`가 전근대로부터의 탈피를 강조하고 `전통`을 개조하려고 한다면, 다시 전통을 강조하고 복원하려고 하는 것은 `전근대로의 회귀`일 수 있다. 그러나 그것은 `근대`에 대한 저항이라는 면에서 또한 `탈근대적 현상`이라고 볼 수도 있다. 또한 1941년 당시 조계종은 일본불교의 영향으로 일본불교와 문화적 혼종성 역시 갖고 있었다. 이렇게 파악된 한국불교의 근대성은 `혼종적 근대성(hybrid modernity)` 혹은 `식민지 근대성(colonial modernity)`이라 할 수 있다.
Statins induce angiogenesis, neurogenesis, and synaptogenesis after stroke (2003)

Abstract We demonstrate that the 3‐hydroxy‐3‐methyl‐glutaryl‐coenzyme A (HMG‐CoA) reductase inhibitors atorvastatin and simvastatin enhance functional outcome and induce brain plasticity when administered after stroke to rats. With atorvastatin treatment initiated 1 day after stroke, animals exhibited significant increases in vascular endothelial growth factor, cyclic guanosine monophosphate, angiogenesis, endogenous cell proliferation and neurogenesis, and an increase in the synaptic protein, synaptophysin. Atorvastatin‐induced angiogenesis in a tube formation assay was reduced by an antibody against the vascular endothelial growth factor receptor 2 (FIK‐1) and by the nitric oxide synthase inhibitor, N ‐mono‐methyl‐ L ‐arginine (L‐NAME). Atorvastatin also induced phosphorylation of Akt and Erk in cultured primary cortical neurons. These data indicate that atorvastatin induced brain plasticity and has neurorestorative activity after experimental stroke. Ann Neurol 2003
Perceptually optimized MPEG compression of synthetic video sequences (2005)

This paper addresses the problem of improving the quality performance of synthetic video sequences by means of standard frame-based coders. The proposed technique can exploit both the knowledge of the 3D model and the intermediate information computed during the rendering process. Firstly, objects are classified, either semantically or automatically, according to their importance. Then the object classification is translated into a macroblock classification, with particular attention to object boundaries. The classification influences the encoder parameters selection, for instance, the quantization parameter. In order to maximize the performance, we propose a rate-distortion formulation of the problem. Experimental results compared with model-unaware encoding show that the proposed techniques can deliver consistent visual quality improvements for different synthetic scenarios using the same bitrate or even less. Demo sequences are available at http://media.polito.it/perceptual3d.
Promoter methylation profiling of 30 genes in human malignant melanoma (2004)

Aberrant methylation and demethylation of promoter CpG islands lead to silencing of tumor-suppressor genes and abnormal expression of normally methylated genes, respectively. Here, we analyzed human melanomas for their methylation and demethylation profiles. Methylation status of core regions in promoter CpG islands was examined for 20 (candidate) tumor-suppressor genes, 4 genes that are not considered as tumor-suppressors, but are frequently silenced in human cancers, and 6 normally methylated melanoma antigen genes (MAGEs). Analysis of 13 melanoma cell lines and 2 cultured normal human epidermal melanocytes (HEMs) showed that 9 tumor-suppressor genes and all 4 non-tumor-suppressor genes were methylated in at least 1 cell line, but never in HEMs, and that all 6 MAGE genes were demethylated in 3 to 13 cell lines. Interestingly, we detected no methylation of MGMT, PTEN, MTAP and p27, which were previously reported as silenced in melanomas. Furthermore, 3 genes that were frequently methylated in the cell lines and 6 MAGE genes were analyzed in 25 surgical melanoma samples. RARB, RASSF1A and 3-OST-2 were methylated in 5 (20%), 9 (36%) and 14 (56%) samples, respectively. MAGE-A1, A2, A3, B2, C1 and C2 were demethylated in 9 (36%), 22 (88%), 20 (80%), 7 (28%), 21 (84%) and 16 (64%) samples, respectively. At least 1 gene was methylated in 18 (72%) samples and at least 1 was demethylated in 24 (96%) samples. No correlation between frequent methylation and frequent demethylation was observed. These profiles showed that both aberrant methylation and demethylation occur widely in human melanomas.