gebhart/patrepeval huggingface dataset:
AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments (2016)

Aptamers, short synthetic RNA/DNA molecules binding specific targets with high affinity and specificity, are utilized in an increasing spectrum of bio-medical applications. Aptamers are identified in vitro via the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol. SELEX selects binders through an iterative process that, starting from a pool of random ssDNA/RNA sequences, amplifies target-affine species through a series of selection cycles. HT-SELEX, which combines SELEX with high throughput sequencing, has recently transformed aptamer development and has opened the field to even more applications. HT-SELEX is capable of generating over half a billion data points, challenging computational scientists with the task of identifying aptamer properties such as sequence structure motifs that determine binding. While currently available motif finding approaches suggest partial solutions to this question, none possess the generality or scalability required for HT-SELEX data, and they do not take advantage of important properties of the experimental procedure. We present AptaTRACE, a novel approach for the identification of sequence-structure binding motifs in HT-SELEX derived aptamers. Our approach leverages the experimental design of the SELEX protocol and identifies sequence-structure motifs that show a signature of selection. Because of its unique approach, AptaTRACE can uncover motifs even when these are present in only a minuscule fraction of the pool. Due to these features, our method can help to reduce the number of selection cycles required to produce aptamers with the desired properties, thus reducing cost and time of this rather expensive procedure. The performance of the method on simulated and real data indicates that AptaTRACE can detect sequence-structure motifs even in highly challenging data.
Identification of Prognostic Factors in Early Unfavorable Stage Hodgkin’s Lymphoma (HL): An Individual Patient Data Meta-Analysis. (2006)

Abstract Background: In patients with early unfavorable stage HL, generally defined as stage I and II patients with mediastinal bulk, elevated ESR, 3 3 involved nodal regions, older age or extranodal involvement, progression-free-survival (PFS) is low compared to patients with early favorable or advanced stages disease. This indicates suboptimal treatment strategies and clinical heterogeneity within the group of patients with early unfavorable stage HL. An international collaborative study was initiated to identify factors that may predict for poor prognosis in this patient group. Methods: Medline and Cochrane Library were systematically searched for randomized controlled trials (n&gt;100 patients per study arm) in early stage HL patients with one or more risk factors receiving 4–6 cycles of ABVD or similar chemotherapy plus radiotherapy. Individual patient data were collected and risk factors for PFS (including disease progression, relapse or death) identified using multivariate analysis (linear stepwise proportional hazards) stratified by study. Results: Six studies were identified; data from 4,490 adult patients enrolled between 08/1982 and 01/2003 were available for analysis. The median follow up was 64 months; 663 patients experienced an event leading to an overall 5-year PFS rate of 85% (95% CI 83%–88%). Six factors were significantly (P&lt;0.01) associated with poor PFS: male gender (Hazard ratio (HR) 1.69), age (HR per additional life year 1.03), B symptoms (HR 1.25), anemia (HR per 1 g/dL Hb decrease 1.09), WBC (HR per 1000 WBC increase 1.02) and large mediastinal tumor (HR 1.54). Split into quintiles by predicted risk, observed 5-year PFS rates differed significantly (p&lt;0.001): 80% of patients with early unfavorable stage HL achieved 5-year PFS rates ranging from 84% (95% CI 81%–87%) to 92% (95% CI 90%–94%) while 20% of patients had poor 5-year PFS, i.e. 76% (95% CI 73%–79%). Compared to low risk patients, those with high risk were more often male (81% vs 40%), older (median age 50 vs 29 years) and presented more often with B symptoms (62% vs 28%) and large mediastinal tumor (42% vs 27%). These data show that among stage I and II patients with at least one risk factor heterogeneity exists. Conclusion: Using basic characteristics and routine tests, it is possible to identify a subgroup of early unfavorable stage patients with poor PFS while receiving 4–6 cycles of ABVD or similar chemotherapy plus radiotherapy. For these patients, treatment optimization is open to discussion in particular when compared to that of patients with advanced stage disease.
Mitigation of combined PMD- and crosstalk-induced signal distortions in spatially-multiplexed multi-core fiber networks (2012)

We investigate the performance of optical equalization of combined PMD- and crosstalk-induced distortions in 112 Gbit/s multi core fiber systems. The residual mean OSNR penalties are reduced to &lt; 0.1 dB.
Room-Temperature Low-Threshold GaAs/InGaAs Photonic Crystal Laser (2007)

We demonstrate GaAs-photonic-crystal laser that can operate at room-temperature with ultra-low-threshold power. These advances are achieved by passivating structures to reduce nonradiative surface recombination loses, which we show as important as Q for threshold determination.
Joint Spectrum Allocation and Structure Optimization in Green Powered Heterogeneous Cognitive Radio Networks (2017)

We aim at maximizing the sum rate of secondary users (SUs) in OFDM-based Heterogeneous Cognitive Radio (CR) Networks using RF energy harvesting. Assuming SUs operate in a time switching fashion, each time slot is partitioned into three non-overlapping parts devoted for energy harvesting, spectrum sensing and data transmission. The general problem of joint resource allocation and structure optimization is formulated as a Mixed Integer Nonlinear Programming task which is NP-hard and intractable. Thus, we propose to tackle it by decomposing it into two subproblems. We first propose a sub-channel allocation scheme to approximately satisfy SUs' rate requirements and remove the integer constraints. For the second step, we prove that the general optimization problem is reduced to a convex optimization task. Considering the trade-off among fractions of each time slot, we focus on optimizing the time slot structures of SUs that maximize the total throughput while guaranteeing the rate requirements of both real-time and non-real-time SUs. Since the reduced optimization problem does not have a simple closed-form solution, we thus propose a near optimal closed-form solution by utilizing Lambert-W function. We also exploit iterative gradient method based on Lagrangian dual decomposition to achieve near optimal solutions. Simulation results are presented to validate the optimality of the proposed schemes.
Core-level photoemission measurements of valence-band offsets in highly strained heterojunctions: Si-Ge system (1989)

The binding-energy separation between the Si 2p and Ge 3d core levels has been measured on pseudomorphically strained heterojunctions consisting of Si on Ge(100) and Ge on Si(100) using x-ray photoemission. Analysis shows that the core-level binding energies referenced to the top of the valence band depend explicitly on strain. As a consequence, the use of core-level data from unstrained materials is inappropriate for determining valence-band offsets in highly strained heterojunctions. Our data have been supplemented by calculations of the relative core--valence-band deformation potentials. These results, together with the calculated uniaxial component of the valence-band splitting and the measured ${E}_{\mathrm{Si}2\mathrm{p}\mathrm{\ensuremath{-}}{E}_{\mathrm{Ge}3\mathit{d}}}$ energy difference on strained heterojunctions, allow us to estimate valence-band offsets of 0.74\ifmmode\pm\else\textpm\fi{}0.13 and 0.17\ifmmode\pm\else\textpm\fi{}0.13 eV for Ge on Si(100) and Si on Ge(100), respectively.
SDNShield: NFV-Based Defense Framework Against DDoS Attacks on SDN Control Plane (2021)

Software-defined networking (SDN) is increasingly popular in today&#x2019;s information technology industry, but existing SDN control plane is insufficiently scalable to support on-demand, high-frequency flow requests. Weaknesses along SDN control paths can be exploited by malicious third parties to launch distributed denial-of-service (DDoS) attacks against the SDN control plane. Recently proposed solutions only partially solve the problem, by protecting either the SDN network edges or the centralized controller. We propose SDNShield, a solution based on emerging network function virtualization (NFV) technologies, which enforces more comprehensive defense against potential DDoS attacks on SDN control plane. SDNShield incorporates a three-stage overload control scheme. The first stage statistically identifies legitimate flows with low complexity and performance overhead. The second stage further performs in-depth TCP handshake verification to ensure good flows are eventually served. The third stage intellectually salvages the misclassified legitimate flows that are falsely dropped from the first two stages. Prototype tests and real data-driven simulation results show that SDNShield can achieve high resilience against brute-force attacks, and maintain good flow-level service quality at the same time.
Magnetic and transport properties of Ni81Fe19∕Al2O3 granular multilayers approaching the superparamagnetic limit (2007)

The magnetic and transport properties of Ni81Fe19∕Al2O3 granular multilayer films were studied in relation to their structural properties as the nominal thickness t of the permalloy (Ni81Fe19) layer was varied near the percolation limit: in the range of 8⩽t⩽16Å while keeping the nominal thickness of the Al2O3 layers constant at 16Å. A good structural quality of the multilayers was demonstrated by low angle x-ray reflectivity measurements, and transmission electron microscopy showed the transition from continuous permalloy layers separated by aluminium oxide layers for t=16Å to metal grains dispersed in the insulator at t=8Å. Magnetization measurements showed the gradual transition from ferromagnetic layers to superparamagnetic clusters and grains that successively become blocked as the temperature decreases. A strong correlation between transport and structural properties was observed in the temperature (T) dependence of the electrical resistance measured with the current in the plane in the range of 2⩽T⩽300K: a gradual change of behavior from continuous permalloy layers with conducting interlayer connections for t=16Å to isolated permalloy grains in a dielectric for the film with t=10Å. The percolation occurs between 12 and 10Å, as deduced both from the magnetic and resistive properties. The discontinuous metal films were analyzed within models for thermally assisted tunneling, yielding estimates of the tunneling barrier for intralayer conduction of about 20meV for t=10Å. A significant magnetic field dependence of the resistance increasing with decreasing temperature was observed in all samples.
Mechanisms of Hepatitis C Virus Clearance by Interferon and Ribavirin Combination (2014)

Hepatitis C virus (HCV) is an enveloped, positive-stranded RNA virus that belongs to the Flaviviridae family. The antiviral mechanisms of interferon and ribavirin also target the highly conserved 5'- untranslated region (UTR). The HCV genome contains a large ORF encoding for a 3011 amino acid-long polyprotein, which is proteolytically processed at the endoplasmic reticulum membrane into ten different mature viral proteins by cellular and viral proteases. The 5'-UTR binds to host ribosomes to translate the HCV polyprotein using an internal ribosome entry site (IRES) mechanism. A number of viruses utilize the IRES mechanism for gene expression, which is distinct from capdependent translation of cellular genes. Cloning and sequencing of the HCV genome has increased our understanding of the HCV molecular virology and led to model systems to study viral replication and develop antiviral drugs. HCV infection is initiated by the attachment and entry of virus particles into host cells by receptor-mediated endocytosis.
A low cost, disposable, zero insertion force cable connector for trial spinal cord stimulation (2003)

A low cost, disposable, zero insertion force cable connector used to connect a implantable electrical stimulation lead to a diagnostic cable is described. The stimulation lead can be inserted into the connector with the lead steering mechanism (stylet) installed. Accessibility to the lead placement steering mechanism allows optimal flexibility for lead placement and stimulation testing. The stylet can be rotated (without rotating the trial stimulation cable), removed, reinserted or replaced with a contoured mechanism without breaking the electrical connection. The handle of the stylet is easy to rotate with simple finger manipulations. When a contoured stylet is rotated, and the lead is held static, the tip of the stimulation lead can be easily directed. Once the steering direction has been established the straight stylet can be reinserted. This may be repeated as many times as required, therefore improving placement accuracy and reduced lead implantation time.
Optimising T cell (re)boosting strategies for adenoviral and modified vaccinia Ankara vaccine regimens in humans (2020)

Simian adenoviral and modified vaccinia Ankara (MVA) viral vectors used in heterologous prime-boost strategies are potent inducers of T cells against encoded antigens and are in advanced testing as vaccine carriers for a wide range of infectious agents and cancers. It is unclear if these responses can be further enhanced or sustained with reboosting strategies. Furthermore, despite the challenges involved in MVA manufacture dose de-escalation has not been performed in humans. In this study, healthy volunteers received chimpanzee-derived adenovirus-3 and MVA vaccines encoding the non-structural region of hepatitis C virus (ChAd3-NSmut/MVA-NSmut) 8 weeks apart. Volunteers were then reboosted with a second round of ChAd3-NSmut/MVA-NSmut or MVA-NSmut vaccines 8 weeks or 1-year later. We also determined the capacity of reduced doses of MVA-NSmut to boost ChAd3-NSmut primed T cells. Reboosting was safe, with no enhanced reactogenicity. Reboosting after an 8-week interval led to minimal re-expansion of transgene-specific T cells. However, after a longer interval, T cell responses expanded efficiently and memory responses were enhanced. The 8-week interval regimen induced a higher percentage of terminally differentiated and effector memory T cells. Reboosting with MVA-NSmut alone was as effective as with ChAd3-NSmut/MVA-NSmut. A ten-fold lower dose of MVA (2 × 10<sup>7</sup>pfu) induced high-magnitude, sustained, broad, and functional Hepatitis C virus (HCV)-specific T cell responses, equivalent to standard doses (2 × 10<sup>8</sup> pfu). Overall, we show that following Ad/MVA prime-boost vaccination reboosting is most effective after a prolonged interval and is productive with MVA alone. Importantly, we also show that a ten-fold lower dose of MVA is as potent in humans as the standard dose.
A Frequency Stabilized Semiconductor Mode-locked Laser with a Phase Modulator and an Intra-cavity Etalon (2010)

A semiconductor laser is mode-locked by phase modulation at one-half the free spectral range of an intra-cavity etalon. The optical comb-lines are locked to the transmission peaks of the etalon using a Pound-Drever-Hall scheme.
Video 8 from Autocrine Fibronectin Inhibits Breast Cancer Metastasis (2023)

&lt;p&gt;FN-depleted Ca1h cells (shFN32) cannot facilitate the migration of Ca1a cells (labeled in red) off of the solid support of the scaffold.&lt;/p&gt;
Improving Animal Disease Detection Through an Enhanced Passive Surveillance Platform (2016)

The ability to rapidly detect and report infectious diseases of domestic animals and wildlife is paramount to reducing the size and duration of an outbreak. There is currently a need in the United States livestock industry for a centralized animal disease surveillance platform, capable of collecting, integrating, and analyzing multiple data streams with dissemination to end-users. Such a system would be disease agnostic and establish baseline information on animal health and disease prevalence; it would alert health officials to anomalies potentially indicative of emerging and/or transboundary disease outbreaks, changes in the status of endemic disease, or detection of other causative agents (eg, toxins). As a part of its mission to accelerate and develop countermeasures against the introduction of emerging and/or transboundary animal diseases into the United States, the Department of Homeland Security is leading and investing in the development of an enhanced passive surveillance platform capable of establishing animal health baselines over time and alerting health officials to potential infectious disease outbreaks or other health anomalies earlier, allowing for more rapid response, improved animal health, and increased economic security.
Embryonic development in the reduced folate carrier knockout mouse is modulated by maternal folate supplementation (2008)

High doses of daily maternal folate supplementation during embryonic/fetal development are necessary for early postimplantation embryonic viability of RFC1 nullizygous embryos, and play a critical role in chorioallantoic fusion, erythropoiesis, and proper development of the neural tube, limbs, lungs, heart, and skin.
Efficacy of hematopoietic cell transplantation in metachromatic leukodystrophy: the Dutch experience (2016)

To the editor:

Metachromatic leukodystrophy (MLD) is a neurodegenerative disorder caused by deficiency of arylsulfatase A,[1][1] leading to sulfatide accumulation and subsequent demyelination of the central and peripheral nervous system.[2][2],[3][3]

MLD is divided into 3 subtypes, based on the
In Vitro Study on the Influence of N-Chlorotaurine on the Ciliary Beat Frequency of Nasal Mucosa (2003)

These results confirm the very low toxic potential of NCT, and they are fundamental for clinical investigations regarding its topical application in the nasal and paranasal sinuses.
Optimal Design of Distributed Sensors and Actuators Made of Smart Materials for Active Vibration Control (2005)

We describe a design technique for optimal control in active structural vibration damping using smart materials. The vibration of a cantilever beam is stabilized by using distributed sensors and actuators. We model the beam by the Timoshenko beam model together with the distributed sensors and actuators. A control law using the weighted integration of vibration velocity is incorporated in the closed loop system. We propose a method to find the optimal layout design of the smart material so as to maximize the damping effect. An objective functional is defined based on the vibration energy of the system. The optimal shapes of the sensor and actuator are determined through minimizing the energy functional of the beam over the admissible shape function space subject to certain geometric constraints. An algorithm has been developed to determine the optimal sensor and actuator layout. This method can be generalized to the plate damping problem and more complicated structures as well.
ChemInform Abstract: STEREOSPECIFIC INTERACTION OF DIPEPTIDE AMIDES WITH DNA, EVIDENCE FOR PARTIAL INTERACTION AND BENDING OF THE HELIX (1975)

Abstract Es wird die Wechselwirkung zwischen den diastereomeren Dipeptidamiden Lys‐Phe und L‐Lys‐D‐Phe und DNS untersucht.
Differenzielle Expression des TRAIL/TRAIL-Rezeptor Systems in Patienten mit chronisch entzündlichen Darmerkrankungen (2008)

Hintergrund: TRAIL induziert Apoptose in Tumorzellen aber nicht in den meisten normalen Zellen. Man nimmt an, dass TRAIL in normalem Gewebe eine wichtige Rolle in der Regulation von Zellfunktionen spielt und als Immunmodulator dient. Neuere Studien belegen, dass das TRAIL/TRAIL-Rezeptor System zudem an der Homeostase von Immunzellen beteiligt ist. Es ist bekannt, dass insuffiziente Apoptose von Lymphozyten und Monozyten durch Apoptose-Resistenz einen der Faktoren für die Entwicklung von chronisch entzündlichen Darmerkrankungen (CED) darstellt. Ebenfalls konnte ein erhöhtes Vorkommen von langlebigen, IgG-produzierenden Plasmazellen bei CED-Patienten beobachtet werden. Hierbei könnte eine Überproduktion von IgG im Verhältnis zu IgA und Matrix Metalloproteinase-3 eine Rolle spielen. Um eine mögliche therapeutische Rolle von TRAIL-Antagonisten in CED aufzudecken, untersuchten wir die Expression des TRAIL/TRAIL-Rezeptor Systems in Darmbiopsien von Patienten mit Morbus Crohn, Colitis ulcerosa, akuter Appendizitis und gesundem Kolon.
An Introduction to the Compute Express Link (CXL) Interconnect (2023)

The Compute Express Link (CXL) is an open industry-standard interconnect between processors and devices such as accelerators, memory buffers, smart network interfaces, persistent memory, and solid-state drives. CXL offers coherency and memory semantics with bandwidth that scales with PCIe bandwidth while achieving significantly lower latency than PCIe. All major CPU vendors, device vendors, and datacenter operators have adopted CXL as a common standard. This enables an inter-operable ecosystem that supports key computing use cases including highly efficient accelerators, server memory bandwidth and capacity expansion, multi-server resource pooling and sharing, and efficient peer-to-peer communication. This survey provides an introduction to CXL covering the standards CXL 1.0, CXL 2.0, and CXL 3.0. We further survey CXL implementations, discuss CXL's impact on the datacenter landscape, and future directions.
Recent advances in the understanding of the interaction of antidepressant drugs with serotonin and norepinephrine transporters (2009)

The biogenic monoamine transporters are integral membrane proteins that perform active transport of extracellular dopamine, serotonin and norepinephrine into cells. These transporters are targets for therapeutic agents such as antidepressants, as well as addictive substances such as cocaine and amphetamine. Seminal advances in the understanding of the structure and function of this transporter family have recently been accomplished by structural studies of a bacterial transporter, as well as medicinal chemistry and pharmacological studies of mammalian transporters. This feature article focuses on antidepressant drugs that act on the serotonin and/or the norepinephrine transporters. Specifically, we focus on structure-activity relationships of these drugs with emphasis on relationships between their molecular properties and the current knowledge of transporter structure.
Tightlip: keeping applications from spilling the beans (2007)

Access control misconfigurations are widespread and can result in damaging breaches of confidentiality. This paper presents TightLip, a privacy management system that helps users define what data is sensitive and who is trusted to see it rather than forcing them to understand or predict how the interactions of their software packages can leak data. The key mechanism used by TightLip to detect and prevent breaches is the doppelganger process. Doppelgangers are sandboxed copy processes that inherit most, but not all, of the state of an original process. The operating system runs a doppelganger and its original in parallel and uses divergent process outputs to detect potential privacy leaks. TightLip is compatible with legacy-code and provides complete, continuous protection at a modest performance cost. SpecWeb99 results show that Apache running on the TightLip prototype exhibits a negligible 5% slowdown in request rate, response time, and transfer rate compared to an unmodified server environment. 1