gebhart/patrepeval huggingface dataset:
Systems Level Analysis and Identification of Pathways and Networks Associated with Liver Fibrosis (2014)

Toxic liver injury causes necrosis and fibrosis, which may lead to cirrhosis and liver failure. Despite recent progress in understanding the mechanism of liver fibrosis, our knowledge of the molecular-level details of this disease is still incomplete. The elucidation of networks and pathways associated with liver fibrosis can provide insight into the underlying molecular mechanisms of the disease, as well as identify potential diagnostic or prognostic biomarkers. Towards this end, we analyzed rat gene expression data from a range of chemical exposures that produced observable periportal liver fibrosis as documented in DrugMatrix, a publicly available toxicogenomics database. We identified genes relevant to liver fibrosis using standard differential expression and co-expression analyses, and then used these genes in pathway enrichment and protein-protein interaction (PPI) network analyses. We identified a PPI network module associated with liver fibrosis that includes known liver fibrosis-relevant genes, such as tissue inhibitor of metalloproteinase-1, galectin-3, connective tissue growth factor, and lipocalin-2. We also identified several new genes, such as perilipin-3, legumain, and myocilin, which were associated with liver fibrosis. We further analyzed the expression pattern of the genes in the PPI network module across a wide range of 640 chemical exposure conditions in DrugMatrix and identified early indications of liver fibrosis for carbon tetrachloride and lipopolysaccharide exposures. Although it is well known that carbon tetrachloride and lipopolysaccharide can cause liver fibrosis, our network analysis was able to link these compounds to potential fibrotic damage before histopathological changes associated with liver fibrosis appeared. These results demonstrated that our approach is capable of identifying early-stage indicators of liver fibrosis and underscore its potential to aid in predictive toxicity, biomarker identification, and to generally identify disease-relevant pathways.
An Experimentally Convenient Preparation of Highly Substituted Pyridines (1990)

Abstract A four step sequence is described for the conversion of α,β-unsaturated carboxylic acids into highly substituted pyridines.
Figure S3. SF3 Xcelligence data from Differential Effects of Clinically Relevant N- versus C-Terminal Truncating CDKN1A Mutations on Cisplatin Sensitivity in Bladder Cancer (2023)

&lt;p&gt;Figure S3: SW780 and RT4 cells are sensitized to cisplatin after the loss of p21. SW780 sg12A clone is more sensitive to cisplatin than sg109A clone, whereas in RT4, the sg12A and sg109a clones have similar sensitivities to cisplatin.&lt;/p&gt;
Implementation of the national desalination and water purification technology roadmap : structuring and directing the development of water supply solutions. (2006)

In the United States, economic growth increasingly requires that greater volumes of freshwater be made available for new users, yet supplies of freshwater are already allocated to existing users. Currently, water for new users is made available through re-allocation of xisting water supplies-for example, by cities purchasing agricultural water rights. Water may also be made available through conservation efforts and, in some locales, through the development of ''new'' water from non-traditional sources such as the oceans, deep aquifer rackish groundwater, and water reuse.
Screening for<i>Staphylococcus epidermidis</i>Markers Discriminating between Skin‐Flora Strains and Those Responsible for Infections of Joint Prostheses (2000)

Fifty-four Staphylococcus epidermidis strains responsible for infections of joint prostheses and 23 strains isolated from skin flora were studied for markers of virulence, to discriminate invasive strains from normal flora. They were screened for binding to polystyrene and matrix proteins and for the presence of staphylococcal genes involved in adhesion. The ica operon involved in biofilm formation was the only marker discriminating between these 2 categories of strains.
VM-μCheckpoint: Design, Modeling, and Assessment of Lightweight In-Memory VM Checkpointing (2014)

Checkpointing and rollback techniques enhance reliability and availability of virtual machines and their hosted IT services. This paper proposes VM-μCheckpoint, a light-weight pure-software mechanism for high-frequency checkpointing and rapid recovery for VMs. Compared with existing techniques of VM checkpointing, VM-μCheckpoint tries to minimize checkpoint overhead and speed up recovery by means of copy-on-write, dirty-page prediction and in-place recovery, as well as saving incremental checkpoints in volatile memory. Moreover, VM-μCheckpoint deals with the issue that latency in error detection potentially results in corrupted checkpoints, particularly when checkpointing frequency is high. We also constructed Markov models to study the availability improvements provided by VM-μCheckpoint (from 99 to 99.98 percent on reasonably reliable hypervisors). We designed and implemented VM-μCheckpoint in the Xen VMM. The evaluation results demonstrate that VM-μCheckpoint incurs an average of 6.3 percent overhead (in terms of program execution time) for 50 ms checkpoint intervals when executing the SPEC CINT 2006 benchmark. Error injection experiments demonstrate that VM-μCheckpoint, combined with error detection techniques in RMK, provides high coverage of recovery.
Supplementary Figure Legends 1-4 from The Wnt Target Jagged-1 Mediates the Activation of Notch Signaling by Progastrin in Human Colorectal Cancer Cells (2023)

Supplementary Figure Legends 1-4 from The Wnt Target Jagged-1 Mediates the Activation of Notch Signaling by Progastrin in Human Colorectal Cancer Cells
Phospholamban immunostaining is a highly sensitive and specific method for diagnosing phospholamban p.Arg14del cardiomyopathy (2017)

Phospholamban (PLN) p.Arg14del cardiomyopathy is associated with an increased risk of malignant ventricular arrhythmias and severe heart failure and a poor prognosis from late adolescence. It can be diagnosed in whole heart specimens, but rarely in right ventricular biopsy specimens, by PLN immunohistochemistry showing PLN-containing aggregates concentrated in cardiomyocytes in dense perinuclear aggresomes. The purpose of this study was to determine whether PLN immunohistochemistry can be used to diagnose PLN p.Arg14del cardiomyopathy using apical left ventricular myocardial specimens harvested during left ventricular assist device (LVAD) implantation. At that stage, a genetic diagnosis, which may guide treatment and referral of family members for further investigation, is frequently not established yet. Included were myocardial specimens from 30 diverse genetic cardiomyopathy cases with known variants (9 carriers of the pathogenic PLN p.Arg14del variant, 18 cases with other pathogenic or likely pathogenic variants in cardiomyopathy-related genes, and 3 with only variants of unknown significance). Immunohistochemical analysis revealed typical dense perinuclear globular PLN-positive aggregates, representing aggresomes, in all nine PLN p.Arg14del cases. In 20 non-PLN cases, PLN-staining was absent. In one non-PLN case, one of the two independent observers misinterpreted PLN staining of heavily wrinkled nuclear membranes of cardiomyocytes as perinuclear PLN aggregates. In this genetic cardiomyopathy cohort, PLN Immunohistochemical analysis in LVAD biopsies was found to be a highly sensitive (100%) and specific (95%) method for demonstration of PLN protein aggregates in PLN p.Arg14del cardiomyopathy. In clinical practice, PLN immunohistochemical analysis of LVAD specimens can be of incremental value in the diagnostic workup of this cardiomyopathy, even more so if genetic analysis is not readily available.
Supplementary Data from An Oncolytic Virus Expressing IL15/IL15Rα Combined with Off-the-Shelf EGFR-CAR NK Cells Targets Glioblastoma (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
ARENA:a novel device to evaluate spatial and imagery skills through sounds (2019)

Spatial memory and imagery are high-level cognitive functions influencing everyday life. These processes are ascribed to the working memory system, devoted to the simultaneous maintenance and process of information. Despite the importance of the working memory system on cognitive development, quantitative assessment methods for cognitive deficits in case of visual impairments are lacking. The goal of this work is to present a device we developed for assessing spatial memory and imagery processes in visually impaired children and adults. The device, called Arena, allows to study these specific cognitive processes exploiting the auditory channel. Arena is a set of 25 speakers arranged in the form of a matrix, covered by tactile sensors. The aim of this innovative technology is to design novel ways and clinical procedures to train and study memory along with the ability to properly built spatial mental representations of auditory items.
Post-traumatic Spinal Deformity (2001)

There are approximately 50,000 fractures to the bony spinal column each year in the United States. The vast majority of unstable spinal injuries are recognized early and managed appropriately. Rarely, the initial treatment may have been inadequate, or in less obvious injuries, less aggressive immobilization techniques may have been chosen. This along with continued exposure to physiologic stresses may lead to a gradual post-traumatic deformity that may further impede the functional as well as emotional status of these often already compromised patients. The management of post-traumatic deformity can be extremely challenging. A post-traumatic kyphotic deformity may occur in the cervical, thoracic, thoracolumbar, or lumbar spine, and once appropriate imaging studies are obtained, careful surgical considerations must be undertaken. Surgical intervention is considered if the kyphotic deformity is progressive over time or there is new onset or progression of a neurologic deficit. Surgical procedures include either a posterior or anterior only approach or any variation of a combined anterior or posterior procedure. In most cases a posterior only fusion is often insufficient for optimal correction and stabilization. Although the majority of patients developing a post-traumatic deformity usually occur after spinal column trauma initially treated nonoperatively, several miscellaneous causes of post-traumatic deformity may occur after surgery. These include nonunion, implant failure, Charcot spine, and technical error. The overall outcome after the surgical management of post-traumatic deformity has been satisfactory with better outcomes in the patients treated earlier as opposed to later. Operative complications include the increased risk of neurologic injury because of the draping of the neural elements over the anterior vertebral elements, any pre-existing spinal cord injury, and possible scarring with cord tethering. Trauma to the spinal cord and column is a devastating injury that may be fraught with many complications including post-traumatic deformity. Certainly, the best treatment is prevention with close follow-up and early intervention when needed. Once present, the treatment of post-traumatic deformity follows basic biomechanical principles consisting of re-establishing the integrity of the compromised spinal columns so that spinal stability can be restored.
Differences and similarities in the repair of two benzo[a]pyrenediol epoxide isomer-induced DNA adducts by uvrA, uvrB, and uvrC gene products (1992)

We have determined the role of the uvrA, uvrB, and uvrC genes in Escherichia coli cells in repairing DNA damage induced by three benzo[a]pyrene diol epoxide isomers. Using the phi X174 RF DNA-E. coli transfection system, we have found that BPDE-I or BPDE-II modified phi X174 RF DNA has much lower transfectivity in uvrA, uvrB, and uvrC mutant cells compared to wild type cells. In contrast, BPDE-III modification of phi X174 RF DNA causes much less difference in transfectivity between wild type and uvr- mutant cells. Moreover, BPDE-I and -II-DNA adducts are much more genotoxic than are BPDE-III-DNA adducts. Using purified UVRA, UVRB, and UVRC proteins, we have found that these three gene products, working together, incise both BPDE-I- and BPDE-III-DNA adducts quantitatively and, more importantly, at the same rate. In general, UVRABC nuclease incises on both the 5' (six to seven nucleotides) and 3' (four nucleotides) sides of BPDE-DNA adducts with similar efficiency with few exceptions. Quantitation of the UVRABC incision bands indicates that both of these BPDE isomers have different sequence selectivities in DNA binding. These results suggest that although UVR proteins can efficiently repair both BPDE-I- and BPDE-III-DNA adducts, in vivo the uvr system is the major excision mechanism for repairing BPDE-I-DNA adducts but may play a lesser role in repairing BPDE-III-DNA adducts. It is possible the low lethality of BPDE-III-DNA adducts is due to less complete blockage of DNA replication.(ABSTRACT TRUNCATED AT 250 WORDS)
Effect of Lead Loss and Sheath Structure on Phase Formation and Alignment in (Bi,Pb) <sub>2</sub> Sr <sub>2</sub> Ca <sub>2</sub> Cu <sub>3</sub> O <sub>10+δ</sub> /Ag Composite Conductors (1995)

The effects of metallic constituent evaporation and sheath structure on grain growth and alignment in silver‐sheathed (Bi,Pb) 2 Sr 2 Ca 2 Cu 3 O 10+δ (Bi‐2223)/Ag composites have been investigated by inductively coupled plasma/atomic emission spectroscopy (ICP/AES), X‐ray diffraction, scanning electron microscopy, and energy dispersive X‐ray spectroscopy. Specimens of Bi‐2223/Ag composites fabricated by the oxide‐powder‐in‐tube technique were peeled (opened) lengthwise to expose the ceramic powder core, and then heat‐treated in 0.075 atm of oxygen for selected temperatures and times. The results were compared with those for as‐processed samples with closed silver sheaths treated under identical conditions. ICP/AES analysis indicated that lead was the only metallic element to undergo substantial evaporation during annealing of opened samples. The lead‐release process in parallel with the Bi‐2223 formation reaction had an activation energy of ∼25 kJ/mol. Lead loss from the opened samples resulted in incomplete conversion to Bi‐2223. The combined results show that the silver sheath effectively prevents evaporative lead loss, preserves and promotes densification, and induces texturing of the layered phases.
Total synthesis of racemic sesbanine (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleTotal synthesis of racemic sesbanineJeffrey C. Bottaro and Glenn A. BerchtoldCite this: J. Org. Chem. 1980, 45, 6, 1176Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/jo01294a059https://doi.org/10.1021/jo01294a059research-articleACS PublicationsRequest reuse permissionsArticle Views514Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Parenchymal and vascular Aβ‐deposition and its effects on the degeneration of neurons and cognition in Alzheimer's disease (2008)

The deposition of the amyloid beta-protein (Abeta) is one of the pathological hallmarks of Alzheimer's disease (AD). Abeta-deposits show the morphology of senile plaques and cerebral amyloid angiopathy (CAA). Senile plaques and vascular Abeta-deposits occur first in neocorti-cal areas. Then, they expand hierarchically into further brain regions. The distribution of Abeta plaques throughout the entire brain, thereby correlates with the clinical status of the patients. Imaging techniques for Abeta make use of the hierarchical distribution of Abeta to distinguish AD patients from non-AD patients. However, pathology seen in AD patients represents a late stage of a pathological process starting 10-30 years earlier in cognitively normal individuals. In addition to the fibrillar amyloid of senile plaques, oligomeric and monomeric Abeta is found in the brain. Recent studies revealed that oligomeric Abeta is presumably the most toxic Abeta-aggregate, which interacts with glutamatergic synapses. In doing so, dendrites are presumed to be the primary target for Abeta-toxicity. In addition, vascular Abeta-deposits can lead to capillary occlusion and blood flow disturbances presumably contributing to the alteration of neurons in addition to the direct neurotoxic effects of Abeta. All these findings point to an important role of Abeta and its aggregates in the neurodegenerative process of AD. Since there is already significant neuron loss in AD patients, treatment strategies aimed at reducing the amyloid load will presumably not cure the symptoms of dementia but they may stop disease progression. Therefore, it seems to be necessary to protect the brain from Abeta-toxicity already in stages of the disease with minor neuron loss before the onset of cognitive symptoms.
Mining complex networks: A new challenge for supporting diagnostic decisions (2017)

New technologies are multiplying at an enormous speed and the produced data is not only massive but also complex. In fact, despite the abundance of tools to capture, process and share information (e.g. data) one cannot broadly assume the standard hypothesis that such data are identically and independently distributed (i.i.d.). As a result, proper handling of data is fundamental in order to convert the available observation in to useful information that leads to knowledge and suitable decision making. In this paper, we focus on network data. That is, we introduce the reader to a theoretical perspective concerning the knowledge mining of huge amount of relational information collected in all the network systems which are ubiquitous in our life. In this context, following a numerical evaluation we show the reader how different kind of information can provide a benefit for a typical machine learning problem i.e. classification. The main issue of our investigation is to provide a case where the accuracy of a classification model benefits when considering the additional information given by both network and dissimilarity features. Moreover, we treat a clinical example that will serve as running case for our analysis.
Ultrathin-Layer Chromatography (2002)

The development of ultrathin-layer silica gel plates with a monolithic structure opens up a new dimension in thin-layer chromatography (TLC). The very small layer thickness of approximately 10 microm and the absence of any kind of binder in combination with the framework of this stationary phase lead to new and improved properties of these ultrathin-layer chromatographic (UTLC) silica-gel plates compared with conventional TLC and high-performance TLC (HPTLC) precoated layers. First of all, the advantages of the UTLC plates are the very short migration distances and, in combination with this, the short development times as well as the very low consumption of solvents as the mobile phase in connection with high sensitivity. The separations of amino acids, pesticides, pharmaceutically active ingredients, phenols, and plasticizers effectively demonstrate the possibilities of the new ultrathin-layer silica-gel plates. Furthermore, a comparison of UTLC, HPTLC, and TLC concerning retention behavior, efficiency, detection limits, migration times, and solvent consumption is performed effectively by the separation of caffeine and paracetamol.
An investigation of FT-Raman spectroscopy for quantification of additives to milk (2012)

In this research, four chemicals, urea, ammonium sulfate, dicyandiamide, and melamine, were mixed into liquid nonfat milk at concentrations starting from 0.1% to a maximum concentration determined for each chemical according to its maximum solubility, and two Raman spectrometers-a commercial Nicolet Raman system and an in-house Raman Chemical Imaging (RCI) system-were used to acquire Raman shift spectra for these mixture samples. These chemicals are potential adulterants that could be used to artificially elevate protein measurements of milk products evaluated by the Kjeldahl method. Baseline subtraction was employed to eliminate milk intensity, and the normalized Raman intensity was calculated from the specific Raman shift from the spectrum of solid chemical. Linear relationships were found to exist between the normalized Raman intensity and chemical concentrations. The linear regression coefficients (R<sup>2</sup>) ranged from 0.9111 to 0.998. Although slightly higher R<sup>2</sup> values were calculated for regressions using spectral intensities measured by the Nicolet system compared to those using measurements from the RCI system, the results from the two systems were similar and comparable. A very low concentration of melamine (400 ppm) in milk was also found to be detectable by both systems. Raman sensitivity of Nicolet Raman system was estimated from normalized Raman intensity and slope of regression line in this study. Chemicals (0.2%) were dissolved in milk and detected the normalized Raman intensity. Melamine was found to have the highest Raman sensitivity, with the highest values for normalized Raman intensity (0.09) and regression line slope (57.04).
Coracohumeral Ligament Reconstruction for Patients With Multidirectional Shoulder Instability (2019)

Coracohumeral ligament pathology arises from acute trauma, capsular thickening, or congenital connective tissue disorders within the glenohumeral joint. Recent studies have highlighted the significance of this pathology in multidirectional shoulder instability because insufficiency of the rotator interval has become increasingly recognized and attributed to failed shoulder stabilization procedures. The diagnosis and subsequent treatment of coracohumeral ligament pathology can be challenging, however, because patients usually present with a history of failed surgical stabilization and persistent laxity. At the time of presentation, most patients have undergone failed nonoperative treatments and are indicated for surgical intervention. One of the options for the treatment of coracohumeral ligament pathology is reconstruction. The purpose of this Technical Note is to describe our preferred surgical technique for the reconstruction of the coracohumeral ligament. Research was performed at the Steadman Philippon Research Institute.