gebhart/patrepeval huggingface dataset:
Clinical Features and Colonoscopic Findings of a Case of Angiosarcoma of the Colon (2011)

Purpose: Angiosarcoma of the colon is a very rare malignancy with only a 12 cases reported in the literature. A 69 year old female presented to the ER with two episodes of syncope within one week. The patient lost consciousness while getting up from a chair on the day of admission and one week prior to admission. There was a history of intermittent, diffuse abdominal pain for a 3 week duration, associated with nausea, intermittent emesis, and watery diarrhea with 4-5 bowel movements daily. There was a history of loss of appetite and weight loss of 17 pounds during prior 2 months. Her past medical history was significant for DM, HTN, coronary artery disease, peripheral vascular disease, carotid endarterectomy, and renal artery stenosis. On physical examination; she was pale and in no acute distress. BP was176/89, pulse was 62. The abdomen was soft, not tender or distended with normal bowel sounds and no organomegaly or palpable masses. The rest of physical examination was remarkable for a positive occult blood in the stool and dysmetria on finger to nose testing. Laboratory studies revealed microcytic hypochromic anemia with hemoglobin of 7.8 g/dl. CT of the head showed multiple high attenuation lesions in both cerebral hemispheres and right cerebellum ranging from 6-18 mm in size with extensive surrounding edema (Panel A). CT chest, abdomen, and pelvis demonstrated several tiny nodules in the base of both lungs, in addition to a 2.4cm soft tissue mass in left adrenal gland. Tumor markers including CA19-9, CEA, and CA125 were negative. Colonoscopy was performed and showed erythematous folds in ascending colon with several biopsies taken (panel B). CT-guided biopsy from left adrenal mass was performed on the same day. Pathology from both sites revealed the same tumor which is poorly differentiated angiosarcoma. Immunohistochemical studies were positive for vimentin, CD-117, CD31, CD34, and factor VIII and negative for cytokeratins; the findings that supported the diagnosis. Of note, CD-17 was strongly positive; a finding which suggested the tumor may be responsive to therapy with Imatinib. The diagnosis of angiosarcoma of the colon with metastases was made. In addition to blood transfusion and dexamethazone, she received cranial irradiation and chemotherapy. On follow up, she is still alive after 9 months from first presentation. Angiosarcoma of the colon is a very unusual cause of gastrointestinal bleeding, or abdominal pain. It is an aggressive tumor with distant metastasis at the time of presentation in most of reported cases. The primary treatment is surgery if feasible with adjuvant chemoradiotherapy. The prognosis based on reported cases is very poor with mortality rate of 62% within one year.
Data from Fibrotic Response to Neoadjuvant Therapy Predicts Survival in Pancreatic Cancer and Is Measurable with Collagen-Targeted Molecular MRI (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;To evaluate the prognostic value of posttreatment fibrosis in human PDAC patients, and to compare a type I collagen targeted MRI probe, CM-101, to the standard contrast agent, Gd-DOTA, for their abilities to identify FOLFIRINOX-induced fibrosis in a murine model of PDAC.&lt;/p&gt;Experimental Design:&lt;p&gt;Ninety-three chemoradiation-treated human PDAC samples were stained for fibrosis and outcomes evaluated. For imaging, C57BL/6 and FVB mice were orthotopically implanted with PDAC cells and FOLFIRINOX was administered. Mice were imaged with Gd-DOTA and CM-101.&lt;/p&gt;Results:&lt;p&gt;In humans, post-chemoradiation PDAC tumor fibrosis was associated with longer overall survival (OS) and disease-free survival (DFS) on multivariable analysis (OS &lt;i&gt;P&lt;/i&gt; = 0.028, DFS &lt;i&gt;P&lt;/i&gt; = 0.047). CPA increased the prognostic accuracy of a multivariable logistic regression model comprised of previously established PDAC risk factors [AUC CPA (−) = 0.76, AUC CPA (+) = 0.82]. In multiple murine orthotopic PDAC models, FOLFIRINOX therapy reduced tumor weight (&lt;i&gt;P&lt;/i&gt; &lt; 0.05) and increased tumor fibrosis by collagen staining (&lt;i&gt;P&lt;/i&gt; &lt; 0.05). CM-101 MR signal was significantly increased in fibrotic tumor regions. CM-101 signal retention was also increased in the more fibrotic FOLFIRINOX-treated tumors compared with untreated controls (&lt;i&gt;P&lt;/i&gt; = 0.027), consistent with selective probe binding to collagen. No treatment-related differences were observed with Gd-DOTA imaging.&lt;/p&gt;Conclusions:&lt;p&gt;In humans, post-chemoradiation tumor fibrosis is associated with OS and DFS. In mice, our MR findings indicate that translation of collagen molecular MRI with CM-101 to humans might provide a novel imaging technique to monitor fibrotic response to therapy to assist with prognostication and disease management.&lt;/p&gt;&lt;/div&gt;
Initial Investigation of Reduced Wall Shear Stress in the Pulmonary Arteries of Hypertension Patients Using Phase Contrast MRI (2008)

A number of concomitant factors are thought to contribute to an increase in the mean pulmonary arterial pressure (MPAP) of pulmonary arterial hypertension (PAH) patients, such as increased pulmonary vascular resistance (PVR), increased blood flow (due to septal defects), and a decrease in wall distensibility.[1] This is in contrast to the normal pulmonary circuit, which is characterized by compliant artery walls and a low PVR, resulting in a low MPAP with little flow and pressure wave reflection. The influence of pathologic MPAP’s on proximal hemodynamic factors such as artery size, flow pulse waveforms, and wall shear stress (WSS) is unclear. Since these factors are known pathophysiological stimuli in the production of molecules that alter vascular tone and matrix properties,[2] we set out to quantify the geometry, flow, and WSS of the left, right and main pulmonary arteries (LPA, RPA, &amp; MPA) of control and PAH patients using phase-contrast magnetic resonance imaging (PC-MRI).
Analysis of RNA polymerase III transcription complexes by gel filtration. (1986)

We studied the in vitro assembly and stability of RNA polymerase I11 transcription complexes on the 5 S RNA and tRNAyt genes of Xenopus and the VA genes of adenovirus.Complete and partial assemblies were formed on these genes using transcription factor IIIA from Xenopus ovaries and factors IIIB and IIIC from HeLa cells.The complexes were purified away from unbound factors by filtration through Sepharose 4B columns and then assayed for transcription in the presence of Xenopus polymerase 111.The 5 S gene complexes were also investigated using a postlabeling DNase I footprinting technique that we devised.The binding of factor IIIA to the 5 S gene facilitated the binding of factor IIIC; this subassembly was required for factor IIIB to bind.On the VA I and tRNA genes, factor IIIC alone bound and allowed IIIB to bind.RNA polymerase bound last to form a preinitiation complex, but it was less stably affixed than any of the factors.The complete factor complexes on the 5 S and VA I genes were strikingly stable to brief exposure to high salt concentrations, and the stability of the factor IIIB interaction was limiting.Two modes of IIIC binding were distinguished that differed in stability and specificity.Assembly of the complexes did not require ATP, and faithful transcription occurred when adenyl-5"yl imidodiphosphate was substituted for ATP.RNA polymerase I11 transcribes the genes for several small RNAs in eucaryotic cells, including tRNAs, 5 S RNA, and the adenovirus-encoded VA RNAs.These genes contain an internal control region in place of a conventional upstream promoter (reviewed in Ref. 1).Accurate transcription has been obtained in vitro using cloned genes and cell-free extracts (2-4).Three transcription factors called IIIA, IIIB, and IIIC have been identified in HeLa cell and Xenopus luevis extracts (5, 6), and a component directly analogous to IIIC has been recognized in yeast (7).The Xenopus factor IIIA has been extensively purified (8), whereas IIIB and IIIC have been only partially purified and may contain more than one protein.Transcription of a 5 S RNA gene requires all three factors and RNA polymerase I11 (5, 6).This gene contains a split internal control region located between +50 and +83 (counting from the site of initiation) that was initially demarcated by deletion analysis (9, 10) and refined using linker substitution mutants (11).The Xenopus factor IIIA, a 38,500-dalton polypeptide (12), binds specifically to the region, and muta-
New Vessel Formation in the Central Nervous System During Tumor Growth, Vascular Malformations, and Moyamoya (2006)

In the normal adult brain, blood vessel formation is tightly down-regulated. However, pathologic processes such as brain tumors can increase the proportion of endothelial cells involved in angiogenesis. When this process is initiated, a complex series of timed events result in new vessel formation. In this review, we will describe the process of angiogenesis in the central nervous system. We will discuss the roles of Vascular Endothelial Growth Factor (VEGF), Fibroblast Growth Factor (FGF), Angiopoietins, Platelet Derived Growth Factor (PDGF), and integrins in angiogenesis. We will also look into their significance in disease processes such as neoplasms, arteriovenous malformations (AVM), and Moyamoya disease.
<p>Time-dependent degradation of carbon nanotubes correlates with decreased reactive oxygen species generation in macrophages</p> (2019)

<b>Introduction and objective:</b> With the increase in carbon nanotube-based products on the commercial market, public concern regarding the possible toxicity of these nanomaterials has attracted much attention. Although previous studies found no obvious toxicity related to carbon nanotubes (CNTs), their safety has not been established because long-term evaluation is still needed. In vitro assays are used to understand the toxicity of nanomaterials. However, the data published so far were generated in short-term assays in which cells are continuously exposed to CNTs. Therefore, the objective of this study is to quantitatively assess the relative long-term cytotoxicity and degradation of CNTs after uptake by macrophages. <b>Methods:</b> We used macrophage cell line of RAW 264.7 and primary rat Kupffer cells to investigate macrophage uptake of CNTs as well as their quantity changes up to a relatively late time point after uptake (7 days) by measuring optical absorbance in the near infrared region and Raman spectra of CNTs in the cell lysates. The time-dependent cytotoxicity was evaluated by measuring reactive oxygen species (ROS), glutathione, cell viability, and caspase 3/7 activity in 1-7 days. <b>Results:</b> CNTs were degraded by approximately 25-30% within first 4 days after uptake; however, and no additional degradation occurred for the remainder of the 7-day test period. Generation of ROS by macrophages decreased as CNT degradation occurred, returning to control levels by Day 7. In the meantime, the glutathione level gradually recovered over time. There were no changes in cell viability or caspase 3/7 activation during CNT degradation. <b>Conclusion:</b> These results confirm that degradation of CNTs by macrophages is associated with ROS generation. The data also suggest that CNT cytotoxicity decreases as they are degraded.
Alpha fetoprotein: Physiology and pathology during pregnancy and application to antenatal diagnosis (1973)

Article Alpha fetoprotein: Physiology and pathology during pregnancy and application to antenatal diagnosis was published on January 1, 1973 in the journal Journal of Perinatal Medicine (volume 1, issue 2).
Antiinfective therapy with a small molecule inhibitor of Staphylococcus aureus sortase (2014)

Methicillin-resistant Staphylococcus aureus (MRSA) is the most frequent cause of hospital-acquired infection, which manifests as surgical site infections, bacteremia, and sepsis. Due to drug-resistance, prophylaxis of MRSA infection with antibiotics frequently fails or incites nosocomial diseases such as Clostridium difficile infection. Sortase A is a transpeptidase that anchors surface proteins in the envelope of S. aureus, and sortase mutants are unable to cause bacteremia or sepsis in mice. Here we used virtual screening and optimization of inhibitor structure to identify 3-(4-pyridinyl)-6-(2-sodiumsulfonatephenyl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole and related compounds, which block sortase activity in vitro and in vivo. Sortase inhibitors do not affect in vitro staphylococcal growth yet protect mice against lethal S. aureus bacteremia. Thus, sortase inhibitors may be useful as antiinfective therapy to prevent hospital-acquired S. aureus infection in high-risk patients without the side effects of antibiotics.
Figure S3 from Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer (2023)

&lt;p&gt;Supplemental Figure 3. Testing screen hits in patient-derived xenografts.&lt;/p&gt;
Free radical chemistry. Part 11. Additions of cyclic and acyclic alcohols and diols to hexafluoropropene (2000)

Peroxide and γ-ray initiated reactions of cyclic alcohols, and various cyclic and acyclic diols, with hexafluoropropene are described. Regiospecific additions are observed and structures follow from NMR data. X-Ray crystallography established the structures of some isomers. A variety of polyfluoroalkylated alkenes, dienes and aromatic building-blocks were derived from the polyfluoroalkylated alcohols.
Tackling Immune Targets for Breast Cancer: Beyond PD-1/PD-L1 Axis (2021)

The burden of breast cancer is imposing a huge global problem. Drug discovery research and novel approaches to treat breast cancer have been carried out extensively over the last decades. Although immune checkpoint inhibitors are showing promising preclinical and clinical results in treating breast cancer, they are facing multiple limitations. From an immunological perspective, a recent report highlighted breast cancer as an "inflamed tumor" with an immunosuppressive microenvironment. Consequently, researchers have been focusing on identifying novel immunological targets that can <i>tune up</i> the tumor immune microenvironment. In this context, several novel non-classical immune targets have been targeted to determine their ability to uncouple immunoregulatory pathways at play in the tumor microenvironment. This article will highlight strategies designed to increase the immunogenicity of the breast tumor microenvironment. It also addresses the latest studies on targets which can enhance immune responses to breast cancer and discusses examples of preclinical and clinical trial landscapes that utilize these targets.
Cytostatics. 19. Configurative assignment of diastereomer N,N'-dialkyl-alpha ,alpha '-diphenylethylenediamines by nuclear resonance spectroscopy (1972)

The assignment of the configuration of o-R1C6H4CH(NHR)CH(NHR)C6H4R1-o (I; R = H, Bu, or Me2CHCH2; R1 = H or Cl) by PMR used the different chem. shifts of the ethylene protons (alpha -H) and arom. protons. The meso form exhibited a paramagnetic shift for the arom. protons and a diamagnetic shift for alpha -H compared to the racemic form. Corresponding differences were obsd. in the spectra of the cis and trans forms of II (X = S or H2), prepd. by reaction of I with CS2 or HCHO, resp. In contrast to I the signals of the arom. H of the cis forms of II were situated at higher field and the alpha -H signals at lower field compared to the trans forms owing to the different interactions between arom. rings. and the alpha -protons.
Isolation and localization of transcribed sequences on human chromosome 22 (1995)

Recently, we reported the generation of a heteronuclear (hn) cDNA library from a human x rodent somatic cell hybrid retaining human chromosome 22. Here, we report the characterization and localization of 12 cDNA derived clones from this library. Human-specific cDNA sequences have been selectively amplified by inter-Alu PCR. To exclude Alu transcripts, only clones with inserts larger than 500 bp were analyzed. Ten of the 12 clones were localized by PCR on chromosome 22, with four clones mapping on additional chromosomes. One PCR-localized clone and two additional clones were mapped on chromosome 22 by in situ hybridization. Transcripts in human cells were identified for seven of the eight clones analyzed by RT-PCR. None of the clones showed significant sequence similarities within the GenBank and EMBL databases, indicating that these clones represent previously unknown genes. This is the first report on the isolation of chromosome 22-specific transcripts from a human x rodent somatic cell hybrid.
Noninvasive forward-scattering system for rapid detection, characterization, and identification of Listeria colonies: image-processing and data analysis (2006)

Bacterial contamination by <i>Listeria monocytogenes </i>puts the public at risk and is also costly for the food-processing industry. Traditional methods for pathogen identification require complicated sample preparation for reliable results. Previously, we have reported development of a noninvasive optical forward-scattering system for rapid identification of <i>Listeria</i> colonies grown on solid surfaces. The presented system included application of computer-vision and patternrecognition techniques to classify scatter pattern formed by bacterial colonies irradiated with laser light. This report shows an extension of the proposed method. A new scatterometer equipped with a high-resolution CCD chip and application of two additional sets of image features for classification allow for higher accuracy and lower error rates. Features based on Zernike moments are supplemented by Tchebichef moments, and Haralick texture descriptors in the new version of the algorithm. Fisher's criterion has been used for feature selection to decrease the training time of machine learning systems. An algorithm based on support vector machines was used for classification of patterns. Low error rates determined by cross-validation, reproducibility of the measurements, and robustness of the system prove that the proposed technology can be implemented in automated devices for detection and classification of pathogenic bacteria.
A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers (2023)

ABSTRACT Protein-protein interactions (PPIs) are responsible for the proper function of biological processes and, when dysregulated, commonly lead to disease. PPI stabilization has only recently been systematically explored for drug discovery despite being a powerful approach to selectively target intrinsically disordered proteins and hub proteins, like 14-3-3, with multiple interaction partners. Disulfide tethering is a site-directed fragment-based drug discovery (FBDD) methodology for screening small molecules in a quantitative, high-throughput manner. We explore the scope of the disulfide tethering technology for the discovery of selective fragments as starting points for the development of potent small molecule PPI stabilizers and molecular glues using the hub protein 14-3-3σ. The complexes with 5 biologically and structurally diverse phospho-peptides, derived from the 14-3-3 client proteins ERα, FOXO1, C-RAF, USP8, and SOS1, were screened for hit identification. Stabilizing fragments could be found for 4/5 client complexes with a diversified hit-rate and stabilizing efficacy for the different 14-3-3/client phospho-peptides. Extensive structural elucidation revealed the ability and adaptivity of the peptide to make productive interactions with the tethered fragments as key criterion for cooperative complex formation. We validated eight fragment stabilizers, six of which showed selectivity for one phospho-peptide client, and structurally characterized two nonselective hits and four fragments that selectively stabilized C-RAF or FOXO1. The most efficacious of these fragments increased 14-3-3σ/C-RAF phospho-peptide affinity by 430-fold. Disulfide tethering to the wildtype C38 in 14-3-3σ provided diverse structures for future optimization of 14-3-3/client stabilizers and highlighted a systematic method to discover molecular glues.
Chromosomal distribution of constitutive heterochromatin in eight species of mahseers (Family: Cyprinidae) from India (2013)

The chromosomal distributions of constitutive heterochromatin were analyzed in 8 species of mahseer, namely, Tor chelynoides (McClelland), T. khudree (Sykes), T. mosal mahanadicus (David), T. mussullah (Sykes), T. putitora (Hamilton), T. progeneius (McClelland), T. tor (Hamilton) and Neolissochilus hexagonolepis (McClelland) using C-banding technique. The constitutive heterochromatin bands were observed on several pairs of chromosomes with maximum numbers in T. progeneius (11 pairs), followed by T. putitora (7 pairs), T. mosal mahanadicus (4), T. khudree (3), T. mussullah (3), N. hexagonolepis (3), T. chelynoides (3) and T. tor (2). In all species, the C-bands were observed mainly on p arm with few on centromeric region of chromosomes. This seems to be the characteristic feature for characterization of these species. The presence of similar chromosome numbers (2n=100) with diverse karyotypes in the mahseer species suggests evolution among the species through pericentric inversions and/or heterochromatin processes. The number and location of the heterochromatic bands were found species-specific and thus useful for the cytotaxonomy of these species. The findings of the present study can also help to understand the evolutionary relationships among the mahseer species.
Next-Generation HVAC: Prospects for and Limitations of Desiccant and Membrane-Based Dehumidification and Cooling (2017)

Recently, next-generation HVAC technologies have gained attention as potential alternatives to the conventional vapor-compression system (VCS) for dehumidification and cooling. Previous studies have primarily focused on analyzing a specific technology or its application to a particular climate. A comparison of these technologies is necessary to elucidate the reasons and conditions under which one technology might outperform the rest. In this study, we apply a uniform framework based on fundamental thermodynamic principles to assess and compare different HVAC technologies from an energy conversion standpoint. The thermodynamic least work of dehumidification and cooling is formally defined as a thermodynamic benchmark, while VCS performance is chosen as the industry benchmark against which other technologies, namely desiccant-based cooling system (DCS) and membrane-based cooling system (MCS), are compared. The effect of outdoor temperature and humidity on device performance is investigated, and key insights underlying the dehumidification and cooling process are elucidated. In spite of the great potential of DCS and MCS technologies, our results underscore the need for improved system-level design and integration if DCS or MCS are to compete with VCS. Our findings have significant implications for the design and operation of next-generation HVAC technologies and shed light on potential avenues to achieve higher efficiencies in dehumidification and cooling applications.
Supplementary document for A Recurrent Ising Machine in a Photonic Integrated Circuit - 4538445.pdf (2020)

Supplementary Information
Three-terminal Josephson device with direct bias-current controlled phase difference (1995)

We have fabricated and characterized the Nb/Al-AlO/sub x/-Nb/Al-AlO/sub x/-Nb three-terminal double junction Josephson device in which the phase difference across the whole device is controlled by the tunnel current flowing through one of the junctions. The device reveals current gain about 10 and has good isolation of the input and output circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>