gebhart/patrepeval huggingface dataset:
Transrenal DNA as a Diagnostic Tool: Important Technical Notes (2004)

A bstract : A small portion of DNA from apoptotic cells escapes complete degradation, appears in blood as oligonucleosomal‐size fragments, is excreted in the urine, and can be used for diagnostic purposes. More detailed study revealed that transrenal DNA (Tr‐DNA) belongs to a relatively low molecular‐weight (150–250 bp) fraction, thereby requiring more careful attention to methods employed for purification and analysis. For example, here it is demonstrated that the QIAamp blood kit purifies primarily high molecular‐weight DNA from serum, whereas the Guanidine/Promega Wizard Resin (GITC/WR) method purifies primarily low molecular‐weight DNA. As a result, sensitivity in detection of K‐ RAS mutations in serum of patients with colorectal tumors is significantly higher with DNA isolated with the GITC/WR method than with the QIAamp kit. Amplicon size is also extremely important in analysis of Tr‐DNA, because the shorter the amplicon, the higher is the sensitivity of biomarker detection in Tr‐DNA. One hundred fifty‐seven and 87 bp amplicons were employed for detection of mutant K‐ RAS in DNA isolated from 0.1 mL of urine obtained from 15 patients with pancreatic cancer. Mutant K‐ RAS was found in Tr‐DNA of 3 and 10 patients with the long and short amplicons, respectively. The sensitivity and specificity of detection of mutant sequences are reduced in the presence of high excess of a respective wild‐type allele, but they can be significantly increased through application of enriched polymerase chain reaction (PCR), peptide nucleic acid (PNA) clamped PCR, and/or stencil‐aided mutation analysis (SAMA), based on selective pre‐PCR elimination of wild‐type sequences.
Distributionally chaotic maps are $C^0$-dense (2019)

We prove that the set of maps which exhibit distributional chaos of type 1 (DC1) is $C^0$-dense in the space of continuous self-maps of given any compact topological manifold (possibly with boundary).
Measure of clustering in continuum percolation: Computer-simulation of the two-point cluster function (1989)

The two-point cluster function C2(r1,r2) is determined for a D-dimensional interpenetrable-sphere continuum model from Monte Carlo simulations. C2(r1,r2) gives the probability of finding two points, at positions r1 and r2, in the same cluster of particles, and thus provides a measure of clustering in continuum-percolation systems. A pair of particles are said to be ‘‘connected’’ when they overlap. Results are reported for D=1,2, and 3 at selected values of the sphere number density ρ and of the impenetrability index λ, 0≤λ≤1. The extreme limits λ=0 and 1 correspond, respectively, to the cases of fully penetrable spheres (‘‘Swiss-cheese’’ model) and totally impenetrable spheres.
Weighted hybrid cone beam reconstruction for circular trajectories (2002)

In cone beam computer tomography circular detector trajectories will be one of the standard for projection data acquisition. To achieve a high volume coverage when using these projection data a hybrid cone beam reconstruction technique has been recently introduced. This technique combines the ideas of fan-beam to parallel-beam rebinning for cone beam geometries and a height rebinning in a rectangular virtual detector window to a simple and efficient back projection algorithm. Using this data reorganization a hybrid reconstruction technique can be applied which is based on a combination of full-scan and half-scan reconstruction in a cylindrical reconstruction volume of maximum size for a given radius of the field of view. The introduction of weighted half scan techniques into this framework leads to a decreased cone beam artifact level while keeping the optimal ratio between the reconstructible and irradiated volume of the scanned volume.
AT&T Research at TRECVID 2013 : Surveillance Event Detection (2013)

T his paper present s a gener al surveillance event detection system that participates in the interactive Surveillance Event Detection ( i SED) task of TRECVID 2013 . In the proposed system, a set of spatio - temporal features including Space - Time Interest Points (STIP) and Dense Trajectories are extracted, and a sliding temporal window is empl oyed as the detection unit. Fisher Vector is used to encode lo w - level features as the representation of each sliding window. Both feature - level and decision - level fusion s are used to combine multiple features . In order to deal with the highly imbalanced nature of surveillance data, the system performs detections usin g the CascadeSVMs algorithm according to each specific event and camera view . Two different interactive environments are evaluated, one focuses on high throughput and the other includes related result expansion. In the primary run evaluations, o ur system r anks the top in 2 out of 7 event detection tasks.
Supplementary tables 1 and 2 from Resistance to Anti-VEGF Therapy Mediated by Autocrine IL6/STAT3 Signaling and Overcome by IL6 Blockade (2023)

&lt;p&gt;Supplementary tables 1 and 2&lt;/p&gt;
An Effective Personalized Approach to a Rare Tumor: Prolonged Survival in Metastatic Pancreatic Acinar Cell Carcinoma Based on Genetic Analysis and Cell Line Development (2011)

Acinar cell carcinoma of the pancreas is an uncommon malignancy, accounting for less than 1% of all pancreatic neoplasms. Because of its rarity, only a few retrospective studies are available to help guide management. We report the case of a patient with metastatic ACC who achieved prolonged survival as a result of personalized treatment designed in part on the basis of molecular and in-vitro data collected on analysis of the tumor and a cell line developed from the liver metastasis. To our knowledge, this represents the first human cell line of ACC. The molecular findings on this case and this patient's cell line may be of use in the management of future cases of this rare tumor and allow the identification of potential novel targets for the effective treatment of this disease.
Reimagining T Staging Through Artificial Intelligence and Machine Learning Image Processing Approaches in Digital Pathology (2020)

Tumor stage and grade, visually assessed by pathologists from evaluation of pathology images in conjunction with radiographic imaging techniques, have been linked to outcome, progression, and survival for a number of cancers. The gold standard of staging in oncology has been the TNM (tumor-node-metastasis) staging system. Though histopathological grading has shown prognostic significance, it is subjective and limited by interobserver variability even among experienced surgical pathologists. Recently, artificial intelligence (AI) approaches have been applied to pathology images toward diagnostic-, prognostic-, and treatment prediction-related tasks in cancer. AI approaches have the potential to overcome the limitations of conventional TNM staging and tumor grading approaches, providing a direct prognostic prediction of disease outcome independent of tumor stage and grade. Broadly speaking, these AI approaches involve extracting patterns from images that are then compared against previously defined disease signatures. These patterns are typically categorized as either (1) handcrafted, which involve domain-inspired attributes, such as nuclear shape, or (2) deep learning (DL)-based representations, which tend to be more abstract. DL approaches have particularly gained considerable popularity because of the minimal domain knowledge needed for training, mostly only requiring annotated examples corresponding to the categories of interest. In this article, we discuss AI approaches for digital pathology, especially as they relate to disease prognosis, prediction of genomic and molecular alterations in the tumor, and prediction of treatment response in oncology. We also discuss some of the potential challenges with validation, interpretability, and reimbursement that must be addressed before widespread clinical deployment. The article concludes with a brief discussion of potential future opportunities in the field of AI for digital pathology and oncology.
ChemInform Abstract: Organocatalytic Diastereoselective Dibromination of Alkenes. (2010)

Abstract Optimized reaction conditions are developed for the formation of dibromides.
Effects of the Balance Control of the Affected Lower Extremity on Balance and Gait in Hemiparetic Patients (2008)

Objective: To investigate the effects of balance control of affected lower extremity on berg balance scale and gait in hemiparetic patients, using the newly developed balance control trainer of lower extremity. Method: Thirty five hemiparetic patients who could stand and ambulate more than 10 meters without assist on even surface were included in this study. The balance control trainer of lower extremity was designed to measure weight shift and knee flexion angle of hemiparetic side and to play a game named Board which use these data, so considering the vertical movement of the center of gravity. We measured above three parameters, and also evaluated with clinical tests including berg balance scale (BBS). We evaluated correlations between parameters on the balance control trainer of lower extremity and clinical parameters. Results: Weight shifting to affected side statistically significantly correlated only with BBS. Affected knee flexion had statistically significant correlations with all clinical tests examined, especially 10 meters walking time (10mWT), timed up and go test (TUG), and BBS. Scores earned from board cleaner game also had statistically significant correlations with all clinical tests examined, especially 10mWT, TUG, and BBS. Conclusion: Correlation exists between the ability to control the affected knee measured by balance control trainer of lower extremity and clinical parameters including 10mWT, TUG, and BBS, so we think the balance control trainer can be a useful tool for the evaluation in hemiparetic patients. (J Korean Acad Rehab Med 2008; 32: 394-399)
Targeted disruption of hepcidin in the liver recapitulates the hemochromatotic phenotype (2014)

Hepcidin is a 25-amino-acid peptide demonstrated to be the iron regulatory hormone capable of blocking iron absorption from the duodenum and iron release from macrophages. Mutations affecting hepcidin regulators or the hepcidin gene itself cause hemochromatosis, a common genetic disorder. Hepcidin is produced mainly by the liver, but many cells and tissues express low levels of the hormone. To determine the contribution of these hepcidin-producing tissues in body iron homeostasis, we have developed a new mouse model in which the hepcidin gene can be conditionally inactivated. Here we compare a liver-specific knockout (KO) mouse model with total KO mice. We show that the liver-specific KO mice fully recapitulate the severe iron overload phenotype observed in the total KO mice, with increased plasma iron and massive parenchymal iron accumulation. This result demonstrates that the hepatocyte constitutes the predominant reservoir for systemic hepcidin and that the other tissues are unable to compensate.
Poxviruses Bearing DNA Polymerase Mutations Show Complex Patterns of Cross-Resistance (2022)

Despite the eradication of smallpox four decades ago, poxviruses continue to be a threat to humans and animals. The arsenal of anti-poxvirus agents is very limited and understanding mechanisms of resistance to agents targeting viral DNA polymerases is fundamental for the development of antiviral therapies. We describe here the phenotypic and genotypic characterization of poxvirus DNA polymerase mutants isolated under selective pressure with different acyclic nucleoside phosphonates, including HPMPC (cidofovir), cHPMPC, HPMPA, cHPMPA, HPMPDAP, HPMPO-DAPy, and PMEO-DAPy, and the pyrophosphate analogue phosphonoacetic acid. Vaccinia virus (VACV) and cowpox virus drug-resistant viral clones emerging under drug pressure were characterized phenotypically (drug-susceptibility profile) and genotypically (DNA polymerase sequencing). Different amino acid changes in the polymerase domain and in the 3'-5' exonuclease domain were linked to drug resistance. Changes in the 3'-5' domain emerged earlier than in the polymerase domain when viruses acquired a combination of mutations. Our study highlights the importance of poxvirus DNA polymerase residues 314, 613, 684, 688, and 851, previously linked to drug resistance, and identified several novel mutations in the 3'-5' exonuclease domain (M313I, F354L, D480Y) and in the DNA polymerase domain (A632T, T831I, E856K, L924F) associated with different drug-susceptibility profiles. Furthermore, a combination of mutations resulted in complex patterns of cross-resistance. Modeling of the VACV DNA polymerase bearing the newly described mutations was performed to understand the effects of these mutations on the structure of the viral enzyme. We demonstrated the emergence of drug-resistant DNA polymerase mutations in complex patterns to be considered in case such mutations should eventually arise in the clinic.
Epitaxial growth of YBa2Cu3O7/CeO2/YSZ thin films on silicon-on-insulator substrates (2002)

A silicon-on-insulator (SOI) substrate is a compliant type of substrate because it is possible to grow a wide variety of materials on it with a small lattice mismatch and a small thermal expansion mismatch. It is quite promising in microelectronics applications, such as hybrid semiconductor/superconductor devices. In this paper, a SOI substrate has been used to grow a superconducting thin film. Using in situ pulsed laser deposition, epitaxial YBaCuO (>4000 Å) thin films have been grown on SOI (100) substrates via a multiple buffer layer of CeO2 and yttrium-stabilized zirconium oxide (YSZ). X-ray diffraction analyses have shown that both the YBaCuO films and the multiple buffer layers are c-axis orientated. We have obtained YBa2Cu3O7/CeO2/YSZ multilayers with a critical temperature, Tc, of 88 K and a critical current density, Jc, of 2 × 106 A cm−2 at 77 K.
Corneal haze in course of Fuchs' endothelial dystrophy. (2012)

This article describes the observations obtained with confocal microscopy (CM) on the corneal structure in course of corneal edema in a patient with Fuchs endothelial corneal dystrophy (FD). The patient was a 40 year old male, suffering from second stage FD, in course of corneal edema and bullous keratopathy. The tissue structure was analyzed with CM confoscan CS4 (Nidek Technologies(®), Birmingham, UK) using the 40x mode. The CM has shown the presence of gaps due to corneal edema and a diffuse stromal hyper reflectivity related to the alteration of the extracellular matrix. It has also showed the presence of binucleate cells, assimilable to keratocytes, in cytokinesis which presented a typical fusiform aspect with two highly reflective nuclei awaiting cell division. The total number of cells was much lower than that of healthy control subjects of similar age, sex and race. The CM in this case suggests a significantly lower number of cells, presumably keratocytes, compared to normal range, but mostly it shows the presence of cells undergoing cytokinesis, which witnesses the active processes of collagenogenesis and possible vasculogenesis that represent early stages of loss of the normal corneal transparency.
A minimum-distance search circuit using dual-line PWM signal processing and charge-packet counting techniques (2002)

This CMOS minimum distance search circuit (MDS) realizes pattern matching engines for multi-media and intelligent processing systems. The chip executes highly-parallel computation of Manhattan distances between an input vector and stored multiple reference vectors, and search of the minimum distance among them. Two novel circuit techniques are based on pulse width modulation (PWM) analog-digital merged circuits.
Establishing the validity and reliability of a modified tool for assessing innovative thinking of engineering students (2019)

The goal of this study was to establish the validity and reliability of a self-report tool for assessing individual differences in innovative thinking, based on a modification of the ‘innovative behavior scale’. A five-stage study was conducted among engineering students worldwide, who enrolled in a massive open online course in Nanotechnology and Nanosensors. Content validity was established by a panel of experts in engineering education. Construct validity was established through exploratory and confirmatory factor analysis, indicating a four-factor solution with 13 items loaded above critical level. Known-groups validity revealed differences among learners with distinct expertise. The scale’s stability across populations and over time was confirmed, providing there has been no intentional intervention. Finally, the scale’s concurrent validity was reinforced through data triangulation with actual practice - the fabrication of innovative nanosensors.
Automatic building texture completion (2007)

In this paper a new image completion algorithm, specifically designed to work with building textures, is proposed. It uses high periodicity, inherent to building textures, to estimate a floor size. The usage of this estimate speeds up image completion process, allowing dealing with high texture resolutions, and helps to capture the macrostructure of the texture. Results and some ideas for further improvement are also provided.
A phase I trial of VB-111, a tissue- and condition-specific dual action vascular disruptive and antiangiogenic agent, for treatment of patients with advanced metastatic cancer. (2011)

3038 Background: VB-111 is a tissue and condition specific vascular disrupting and anti-angiogenic agent based on a novel Vascular Targeting System (VTS) which contains the modified angiogenic specific pre-proendothelin promoter, and a FAS/TNF receptor chimeric transgene. Preclinical studies have shown that VB-111 has significant antitumor activity. We report the results of a phase I single-dose escalation study of VB-111 in patients with advanced metastatic solid tumors. Methods: Eligible patients had advanced solid tumors, with no existing curative therapy, and adequate organ function and performance status. VB-111 was administered as a single intravenous infusion at escalating doses ranging from 1X1010 to 1X1013 viral particles in seven successive cohorts. Primary and secondary endpoints were safety and efficacy at 56 days post dosing, respectively. Results: Thirty three patients enrolled in two cancer centers. VB-111 was well tolerated; most patients in Cohorts 5 to 7 developed self-limited fever and chills. Neutralizing antibodies to Ad-5 at baseline were elevated in over half of the patients. Ad-5 DNA blood levels gradually declined within 1 to 56 days post dosing; some patients had up to 103 copies/ µg genomic DNA at day 56. As expected from the specificity of VB-111, no expression of the Fas chimeric transgene in the blood was found. However, in a patient with esophageal cancer, transgene expression was detected in the aspirate from a subcutaneous metastasis 4 and 28 days after treatment. Three out of 14 (21%) evaluable patients in cohorts 1 to 5 vs. 9 out of 18 evaluable patients in cohorts 6 and 7 (50%) had stable disease at day 56. One patient with papillary thyroid carcinoma had PR at 6 months, which persisted for 18 months. Three patients, one with neuroendocrine and two with thyroid carcinoma had a significant decline in tumor-markers. Conclusions: VB-111 was found to be safe, well tolerated and showed some evidence for anti-tumor effect in patients with advanced metastatic cancer at a single administration of up to 1X1013 VPs. Repeat dose administration as well as evaluation in specific tumors will be explored in future studies.
One-Shot Federated Learning for Model Clustering and Learning in Heterogeneous Environments (2023)

We propose a communication efficient approach for federated learn- ing in heterogeneous environments. The system heterogeneity is reflected in the presence of K different data distributions, with each user sampling data from only one of K distributions. The proposed approach requires only one communication round between the users and server, thus significantly reducing the communication cost. Moreover, the proposed method provides strong learning guarantees in heterogeneous environments, by achieving the optimal mean-squared error (MSE) rates in terms of the sample size, i.e., matching the MSE guarantees achieved by learning on all data points belonging to users with the same data distribution, provided that the number of data points per user is above a threshold that we explicitly characterize in terms of system parameters. Remarkably, this is achieved without requiring any knowledge of the underlying distributions, or even the true number of distributions K. Numerical experiments illustrate our findings and underline the performance of the proposed method.
Olfactory Ensheathing Cells: Characteristics, Genetic Engineering, and Therapeutic Potential (2006)

Injured neurons in the mammalian central nervous system (CNS) do not normally regenerate their axons after injury. Neurotrauma to the CNS usually results in axonal damage and subsequent loss of communication between neuronal networks, causing long-term functional deficits. For CNS regeneration, repair strategies need to be developed that promote regrowth of lesioned axon projections and restoration of neuronal connectivity. After spinal cord injury (SCI), cystic cavitations are often found, particularly in the later stages, due to the loss of neural tissue at the original impact site. Ultimately, for the promotion of axonal regrowth in these situations, some form of transplantation will be required to provide lesioned axons with a supportive substrate along which they can extend. Here, we review the use of olfactory ensheathing cells: their location and role in the olfactory system, their use as cellular transplants in SCI paradigms, alone or in combination with gene therapy, and the unique properties of these cells that may give them a potential advantage over other cellular transplants.
Mining Code Review Data to Understand Waiting Times Between Acceptance and Merging: An Empirical Analysis (2022)

Increasing code velocity (or the speed with which code changes are reviewed and merged) is integral to speeding up development and contributes to the work satisfaction of engineers. While factors affecting code change acceptance have been investigated in the past, solutions to decrease the code review lifetime are less understood. This study investigates the code review process to quantify delays and investigate opportunities to potentially increase code velocity. We study the temporal characteristics of half a million code reviews hosted on Gerrit and Phabricator, starting from the first response, to a decision to accept or reject the changes, and until the changes are merged into a target branch. We identified two types of time delays: (a) the wait time from the proposal of code changes until first response, and (b) the wait time between acceptance and merging. Our study indicates that reducing the time between acceptance and merging has the potential to speed up Phabricator code reviews by 29-63%. Small code changes and changes made by authors with a large number of previously accepted code reviews have a higher chance of being immediately accepted, without code review iterations. Our analysis suggests that switching from manual to automatic merges can help increase code velocity.