gebhart/patrepeval huggingface dataset:
The Role of CD4+ Tissue Resident Memory Cells in Oncogene Driven Lung Adenocarcinoma (2021)

Abstract Lung cancer presents a global health risk that is responsible for over 2 million deaths worldwide every year. Tissue resident memory T cells (Trm) are critical for rapid protection to pathogens at entry points in the body, including the lung. Trm are identified as CD69+ CD103+ cells which remain in the tissue (i.e. lung), are longer-lived memory cells, and have antigen specificity. Many studies have shown clinical significance with tumour infiltrating lymphocytes (TIL) markers of CD103+ and CD69+ in solid tumour cancers. Few studies have addressed the direct or indirect mechanism of anti-tumour function of CD4+ Trm cells during tumour progression and how the tumour microenvironment impacts this. One primary role of CD4+ T cells in anti-tumour immunity is to provide aid to CD8+ effector cells. CD4+ Trm are known to have Th1 interferon responses to viral infection and Th2 type responses in allergic response leading to excess fibrosis. Little is known of the diversity of CD4+ Trm and their Type-1 or -2 phenotypes during cancer. In this study, we used a genetically engineered mouse model (GEMM) of lung adenocarcinoma (LAC), with doxycycline-inducible oncogene mutation KRASG12D. We observed a significant increase in PD-1+ CD4+ Trm with a Th2-like phenotype (CD44+ CD62L−CD103+ CD69+ PD-1+GATA3hi) in the KRASG12D tumour bearing lungs. When stimulated ex vivo with PMA/ionomycin, we found CD4+ CD69+ cells produced more IFNγ in the KRASG12DGEMM. To examine clinical relevance, we used the program KMplotter and found signatures of Trm and CD4+ Trm significantly correlated with increased survival in LAC patients. We intend to determine the functional relevance of these Th2-like CD4+ TRM cells in the tumour microenvironment.
Flexible Drift Tube for High Resolution Ion Mobility Spectrometry (Flex-DT-IMS) (2020)

This paper describes, in detail, the development of a novel, low-cost, and flexible drift tube (DT) along with an associated ion mobility spectrometer system. The DT is constructed from a flexible printed circuit board (PCB), with a bespoke "dog-leg" track design, that can be rolled up for ease of assembly. This approach incorporates a shielding layer, as part of the flexible PCB design, and represents the minimum dimensional footprint conceivable for a DT. The low thermal mass of the polyimide substrate and overlapping electrodes, as afforded by the dog-leg design, allow for efficient heat management and high field linearity within the tube-achieved from a single PCB. This is further enhanced by a novel double-glazing configuration which provides a simple and effective means for gas management, minimizing thermal variation within the assembly. Herein, we provide a full experimental characterization of the flexible DT ion mobility spectrometer (Flex-DT-IMS) with corresponding electrodynamic (Simion 8.1) and fluid dynamic (SolidWorks) simulations. The Flex-DT-IMS is shown to have a resolution >80 and a detection limit of low nanograms for the analysis of common explosives (RDX, PETN, HMX, and TNT).
Experimental and Clinical Autogenous Distal Metacarpal Reconstruction (1971)

*Department of Orthopedic Surgery. University of Iowa, Iowa City, Iowa. †Division of Orthopedic Surgery, Albany Medical College, Albany, New York.
Simulated autocorrelations of a broadband signal in an ocean with a layered bottom (1988)

It is well documented that the correlations between the multipath arrivals from a broadband acoustic source in a deep ocean can be greatly affected by the bottom sediment. As an aid to explaining these effects, the seismogram version of the SAFARI model was extended to simulate the autocorrelation of the received signal. As with the original model, the bottom environment is input in the form of a geoacoustic bottom model. However, the inputs to the extended model also include the source level, realistic ambient noise and sea state conditions, noise due to distant shipping, and the self-noise levels of the receiving array. Simulations were carried out using the environment of the Tufts Abyssal Plain of the Northeastern Pacific. The geoacoustic bottom model for this area was developed at DREP [N. R. Chapman, J. Acoust. Soc. Am. 73, 1601–1607 (1983)] and has been validated by a detailed analysis of propagation loss measurements. It was found from these simulations that reflections from both the water-sediment and sediment basement interfaces result in a time-spreading of the correlogram peaks as well as a reduction in the overall correlation magnitude.
Statistical Analysis of Satellite Communication Experimental Time Diversity in Slovenia (2020)

In order to achieve larger capacities needed for modern multimedia services, satellite communications are using high frequencies, such as the Ka/Q bands and above. However, due to several atmospheric factors, in particular rain along the propagation path, communication at these high frequencies are subject to signal attenuation, which limits the availability and reliability of links. To mitigate signal attenuation, several fade mitigation techniques exist. Diversity techniques, such as site diversity, orbital diversity and time diversity, represent one such group. In this paper the performance of time diversity is investigated based on one-year measurement data statistical analyses of rain attenuation from Alphasat satellite at 19.7GHz and 39.4 GHz in Ljubljana. Moreover, the performance of time diversity in two-site diversity system is investigated based on two years experimental signal data from Astra 3B satellite at 20.2GHz measured at three locations in Slovenia.
Statistical analysis of multi-dimensional, temporal gene expression of stem cells to elucidate colony size-dependent neural differentiation (2018)

High throughput gene expression analysis using qPCR is commonly used to identify molecular markers of complex cellular processes. However, statistical analysis of multi-dimensional, temporal gene expression data is complicated by limited biological replicates and large number of measurements. Moreover, many available statistical tools for analysis of time series data assume that the data sequence is static and does not evolve over time. With this assumption, the parameters used to model the time series are fixed and thus, can be estimated by pooling data together. However, in many cases, dynamic processes of biological systems involve abrupt changes at unknown time points, making the assumption of stationary time series break down. We addressed this problem using a combination of statistical methods including hierarchical clustering, change point detection, and multiple testing. We applied this multi-step method to multi-dimensional, temporal gene expression data that resulted from our study of colony size-dependent neural cell differentiation of stem cells. The gene expression data were time series as the observations were recorded sequentially over time. Hierarchical clustering segregated the genes into three distinct clusters based on their temporal expression profiles; change point detection identified specific time points at which the entire dataset was divided into several homogenous subsets to allow a separate analysis of each subset; and multiple testing procedure identified the differentially expressed genes in each cluster within each subset of data. We established that our multi-step approach pinpoints specific sets of genes that underlie colony size-mediated neural differentiation of stem cells and demonstrated its advantages over conventional parametric and non-parametric tests that do not take into account temporal dynamics of the data. Importantly, our proposed approach is broadly applicable to any multivariate data sets of limited sample size from high throughput and high content screening such as in drug and biomarker discovery studies.
Algorithms in C++: Fundamentals, Data Structures, Sorting, Searching (1998)

From the Publisher:
Many new algorithms are presented, and the explanations of each algorithm are much more detailed than in previous editions. A new text design and detailed, innovative figures, with accompanying commentary, greatly enhance the presentation. The third edition retains the successful blend of theory and practice that has made Sedgewick's work an invaluable resource for more than 250,000 programmers!

This particular book, Parts 1n4, represents the essential first half of Sedgewick's complete work. It provides extensive coverage of fundamental data structures and algorithms for sorting, searching, and related applications. Although the substance of the book applies to programming in any language, the implementations by Van Wyk and Sedgewick also exploit the natural match between C++ classes and ADT implementations.
Highlights
Expanded coverage of arrays, linked lists, strings, trees, and other basic data structures Greater emphasis on abstract data types (ADTs), modular programming, object-oriented programming, and C++ classes than in previous editions Over 100 algorithms for sorting, selection, priority queue ADT implementations, and symbol table ADT (searching) implementations New implementations of binomial queues, multiway radix sorting, randomized BSTs, splay trees, skip lists, multiway tries, B trees, extendible hashing, and much more Increased quantitative information about the algorithms, giving you a basis for comparing them Over 1000 new exercises to help you learn the properties of algorithms 

Whether you are learning the algorithms for the first time or wish to have up-to-date reference material that incorporatesnew programming styles with classic and new algorithms, you will find a wealth of useful information in this book.
Printed Aperiodic Cavity for Computational and Microwave Imaging (2016)

We demonstrate a frequency-diverse aperture for microwave imaging based on a planar cavity at K-band frequencies (18-26.5 GHz). The structure consists of an array of radiating circular irises patterned into the front surface of a double-sided printed circuit board. The irises are distributed in a Fibonacci pattern to maximize spatial diversity at the scene. The printed cavity is a phase-diverse system and encodes imaged scene information onto a set of frequencies that span the K-band. Similar to recently reported metamaterial apertures, the printed cavity imager does not require any mechanically moving parts or complex phase shifting networks. Imaging of a number of targets is shown; these reconstructed images demonstrate the ability of the system to perform imaging at the diffraction limit. The proposed printed cavity imager possesses a relatively large quality factor that can be traded off to achieve higher radiation efficiency. The general mode characteristics of the printed cavity suggest advantages when used in computational imaging scenarios.
Sup. Table 2 from Clinical Significance of Pancreatic Atrophy Induced by Immune-Checkpoint Inhibitors: A Case–Control Study (2023)

&lt;p&gt;Supplementary table 2 (AEs of PA patients)&lt;/p&gt;
Pathological, biochemical, and biophysical characteristics of the transthyretin variant Y114H (p.Y134H) explain its very mild clinical phenotype (2015)

Transthyretin (TTR) is a homotetrameric protein that must misfold in order to form amyloid fibrils. Misfolding includes rate limiting tetramer dissociation, followed by fast tertiary structural changes of the monomer that enable aggregation. Hereditary ATTR amyloidosis is an autosomal dominant genetic disorder with systemic deposition of amyloid fibrils induced by TTR gene mutation. We identified a rare Y114H (p.Y134H) TTR variant in a Japanese patient presenting with late-onset, very mild clinical course. The patient had an extremely low serum variant TTR concentration (18% of total TTR), whereas the composition of variant TTR was 55% in amyloid fibrils in tenosynovial tissues obtained at carpal tunnel release surgery. The amyloid fibril deposits in the ATTR Y114H patient had an altered structure compared with that in wild-type ATTR patients, as determined by luminescent conjugated poly/oligo-thiophene fluorescence spectroscopy. Biophysical studies using recombinant protein showed that Y114H TTR was markedly destabilized both thermodynamically and kinetically and was highly amyloidogenic in vitro. These data suggest that extremely low serum variant Y114H TTR concentration, probably due to endoplasmic reticulum-associated degradation of unstable variant TTR protein, protected this patient from severe amyloidosis, as self-assembly of the amyloidogenic intermediate is a concentration-dependent process.
Pathogenesis, diagnosis and management of dentin hypersensitivity: an evidence-based overview for dental practitioners (2020)

Though dentin hypersensitivity (DHS) is one of the most common complaints from patients in dental clinics, there are no universally accepted guidelines for differential diagnosis as well as selection of reliable treatment modalities for this condition. The neurosensory mechanisms underlying DHS remain unclear, but fluid movements within exposed dentinal tubules, i.e., the hydrodynamic theory, has been a widely accepted explanation for DHS pain. As several dental conditions have symptoms that mimic DHS at different stages of their progression, diagnosis and treatment of DHS are often confusing, especially for inexperienced dental practitioners. In this paper we provide an up-to-date review on risk factors that play a role in the development and chronicity of DHS and summarize the current principles and strategies for differential diagnosis and management of DHS in dental practices. We will outline the etiology, predisposing factors and the underlying putative mechanisms of DHS, and provide principles and indications for its diagnosis and management. Though desensitization remains to be the first choice for DHS for many dental practitioners and most of desensitizing agents reduce the symptoms of DHS by occluding patent dentinal tubules, the long-term outcome of such treatment is uncertain. With improved understanding of the underlying nociceptive mechanisms of DHS, it is expected that promising novel therapies will emerge and provide more effective relief for patients with DHS.
How Compressible Are Innovation Processes? (2018)

The sparsity and compressibility of finite-dimensional signals are of great interest in fields, such as compressed sensing. The notion of compressibility is also extended to infinite sequences of independent identically distributed or ergodic random variables based on the observed error in their nonlinear k-term approximation. In this paper, we use the entropy measure to study the compressibility of continuous-domain innovation processes (alternatively known as white noise). Specifically, we define such a measure as the entropy limit of the doubly quantized (time and amplitude) process. This provides a tool to compare the compressibility of various innovation processes. It also allows us to identify an analogue of the concept of “entropy dimension" which was originally defined by Rényi for random variables. Particular attention is given to stable and impulsive Poisson innovation processes. Here, our results recognize Poisson innovations as the more compressible ones with an entropy measure far below that of stable innovations. While this result departs from the previous knowledge regarding the compressibility of impulsive Poisson laws compared with continuous fat-tailed distributions, our entropy measure ranks α-stable innovations according to their tail.
Touch to Play -- Exploring Touch-Based Mobile Interaction with Public Displays (2011)

Mobile interactions with public displays are often indirect and not very convenient for multiple users at the same time. In this paper we use the physical, touch-based interaction with Near Field Communication (NFC) to investigate direct mobile interactions with public displays for multiple users. For that purpose, we adopt the Whack-a-Mole game for dynamic NFC-displays, which combine the physical interaction with NFC-tagged objects and the visual output capabilities of public displays. We show that a grid of NFC-tags can be used to implement direct mobile interaction with public displays in general and a highly interactive multiplayer game in particular. Our study shows that users appreciate this physical, NFC-based mobile interaction, although technical advances are still necessary in order to improve its recognition rate of about 70%. The study also indicates that users are willing to interact with large displays in public, but prefer private or semi-public places, where their interactions attract less attention.
Evidence of leaky protection following COVID-19 vaccination and SARS-CoV-2 infection in an incarcerated population (2023)

Whether SARS-CoV-2 infection and COVID-19 vaccines confer exposure-dependent ("leaky") protection against infection remains unknown. We examined the effect of prior infection, vaccination, and hybrid immunity on infection risk among residents of Connecticut correctional facilities during periods of predominant Omicron and Delta transmission. Residents with cell, cellblock, and no documented exposure to SARS-CoV-2 infected residents were matched by facility and date. During the Omicron period, prior infection, vaccination, and hybrid immunity reduced the infection risk of residents without a documented exposure (HR: 0.36 [0.25-0.54]; 0.57 [0.42-0.78]; 0.24 [0.15-0.39]; respectively) and with cellblock exposures (0.61 [0.49-0.75]; 0.69 [0.58-0.83]; 0.41 [0.31-0.55]; respectively) but not with cell exposures (0.89 [0.58-1.35]; 0.96 [0.64-1.46]; 0.80 [0.46-1.39]; respectively). Associations were similar during the Delta period and when analyses were restricted to tested residents. Although associations may not have been thoroughly adjusted due to dataset limitations, the findings suggest that prior infection and vaccination may be leaky, highlighting the potential benefits of pairing vaccination with non-pharmaceutical interventions in crowded settings.
A randomized, double‐blind, placebo‐controlled trial of pridopidine in Huntington's disease (2013)

We examined the effects of 3 dosages of pridopidine, a dopamine-stabilizing compound, on motor function and other features of Huntington's disease, with additional evaluation of its safety and tolerability. This was a randomized, double-blind, placebo-controlled trial in outpatient neurology clinics at 27 sites in the United States and Canada. Two hundred twenty-seven subjects enrolled from October 24, 2009, to May 10, 2010. The intervention was pridopidine, either 20 (n=56), 45 (n=55), or 90 (n=58) mg daily for 12 weeks or matching placebo (n=58). The primary outcome measure was the change from baseline to week 12 in the Modified Motor Score, a subset of the Unified Huntington's Disease Rating Scale Total Motor Score. Measures of safety and tolerability included adverse events and trial completion on the assigned dosage. After 12 weeks, the treatment effect (relative to placebo, where negative values indicate improvement) of pridopidine 90 mg/day on the Modified Motor Score was -1.2 points (95% confidence interval [CI], -2.5 to 0.1 points; P = .08). The effect on the Total Motor Score was -2.8 points (95% CI, -5.4 to -0.1 points; nominal P = .04). No significant effects were seen in secondary outcome measures with any of the active dosages. Pridopidine was generally well tolerated. Although the primary analysis did not demonstrate a statistically significant treatment effect, the overall results suggest that pridopidine may improve motor function in Huntington's disease. The 90 mg/day dosage appears worthy of further study. Pridopidine was well tolerated.
HLA class II genotyping: two assay systems compared (1995)

In the last few years, a variety of DNA-based human leukocyte antigen (HLA) typing methods have emerged, revealing the extreme polymorphism of HLA genes. This polymorphism makes it difficult for a clinical laboratory to establish the best HLA typing strategy. In this study we have compared two techniques for performing HLA-DRB typing: a commercial rapid assay based on the polymerase chain reaction (PCR) followed by reverse dot-blot hybridization of the PCR products (the Inno-LiPA assay), and a method based on PCR followed by restriction fragment length polymorphism analysis. We found that both methods provide reliable results with a high rate of concordance (97%) and that Inno-LiPA is convenient for large-scale routine typing. However, if a high-resolution allelic typing is required, each method lacks accuracy but using them in association improves the accuracy of the results.
Correction: Electrophysiological findings during re-do procedures after single-shot pulmonary vein isolation for atrial fibrillation with pulsed field ablation (2023)

Figure 5 in the original version of this article has been replaced with the figure as shown below. (Figure presented.) Number of reconnected pulmonary vein at re-do procedure The original article has been corrected.
Transformation of Human Cathelicidin LL-37 into Selective, Stable, and Potent Antimicrobial Compounds (2014)

This Letter reports a family of novel antimicrobial compounds obtained by combining peptide library screening with structure-based design. Library screening led to the identification of a human LL-37 peptide resistant to chymotrypsin. This d-amino-acid-containing peptide template was active against Escherichia coli but not methicillin-resistant Staphylococcus aureus (MRSA). It possesses a unique nonclassic amphipathic structure with hydrophobic defects. By repairing the hydrophobic defects, the peptide (17BIPHE2) gained activity against the ESKAPE pathogens, including Enterococcus faecium, S. aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter species. In vitro, 17BIPHE2 could disrupt bacterial membranes and bind to DNA. In vivo, the peptide prevented staphylococcal biofilm formation in a mouse model of catheter-associated infection. Meanwhile, it boosted the innate immune response to further combat the infection. Because these peptides are potent, cell-selective, and stable to several proteases, they may be utilized to combat one or more ESKAPE pathogens.
Experimental Study on Quantum Structure of Silicon Nano Wire and Its Impact on Nano Wire MOSFET and Single-Electron Transistor (2006)

We fabricated [100] and [110] directed nano wire MOSFET (NWFET), which works as NFET and PFET in the same channel. By comparing [100] and [110] direction, significantly small threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) fluctuation is experimentally observed in [110] PFET for the first time. This result supports the superiority of [110] NW PFET. Extremely narrow NWFET works as single-electron/single-hole transistors (SET/SHT). By comparing [100] and [110] direction, channel direction dependence of Coulomb blockade (CB) oscillations is experimentally clarified for the first time. We realize the highest performance in [100] SHT