gebhart/patrepeval huggingface dataset:
Patent status of the therapeutically important G-protein-coupled receptors (2001)

A paradigm shift has occurred in the post-genomic age where genes are rapidly identified using homology based experimental and computational approaches. The intellectual property (IP) rights to these genes as research tools has changed the nature of what is being patented, by whom and for what purpose. The traditional idea of an invention's commercial value has been altered from having an intrinsic value to having potential value in biomedical research as a therapeutic target. Companies and universities alike are filing patents on discovered genes in order to license them for scientific research or simply to ensure freedom to operate for internal investigation without threat of infringement. The IP of one protein family in particular is the focus of this review. G-protein-coupled receptors are proven to be important drug targets and therefore, the number of patent filings on the genes, proteins and uses of these receptors currently exceeds the number of receptors themselves. A profile of the current patent holdings will be discussed as well as revised guidelines to keep in mind when filing applications on genes and gene products.
Systematic Security Analysis of Stream Encryption With Key Erasure (2021)

We consider a generalized construction of stream ciphers with forward security. The design framework is modular: it is built from a so-called layer function that updates the key and (optionally) the nonce and generates a new pseudorandom output stream. We analyze the generalized construction for four different instantiations: two possible layer functions that are in turn instantiated with either a block cipher or a pseudorandom function. We prove that each of these instantiations gives a stream cipher that is pseudorandom and forward secure in the multi-user setting with a very tight bound. A comprehensive analysis shows that the two block cipher based instantiations achieve very similar bounds. For the pseudorandom function based instantiations there is no clear winner: either layer can be beneficial over the other one, depending on the choice of parameters. By instantiating the pseudorandom function with a generic construction such as the sum of permutations, we obtain a highly efficient and competitive stream cipher based on an n-bit block cipher that is secure beyond the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2^{\text {n}/2}$ </tex-math></inline-formula> birthday bound.
PSIV-20 Impact of OutPace® Feed Additive on nursery pig growth performance: A meta-analysis (2020)

Abstract OutPace® Feed Additive (OP), contains a carefully researched blend of activated medium chain fatty acids (MCFAs; PMI, Arden Hills, MN), formulated to help mitigate the effects of stress in nursery pigs. Several studies using OP in both late and full nursery periods resulted in improved pig performance. A meta-analysis using 9 studies (4 studies during late nursery [15 to 26.8 kg BW] and 5 studies during the full nursery [5.9 to 25.4 kg]) was done to determine the impact of OP (included at 0.25% Phase 1 and 2; 0.125% Phase 3) on average daily gain, average daily feed intake, and feed conversion. The combined data was considered a randomized complete block design. Analysis of variance was completed with mixed models using the GLIMMIX procedure of SAS (SAS 9.4, SAS Institute Inc., Cary, NC) and least squares means were compared using Fisher’s least significant difference (P &amp;lt; 0.05). In the analysis of 5 studies conducted in late nursery (45 pens/treatment of 6 to 20 pigs/pen), pigs provided OP had higher average daily gain (0.67 vs 0.63 kg/d; P &amp;lt; 0.05), increased average daily feed intake (0.99 vs 0.97 kg/d; P &amp;lt; 0.05), and improved feed efficiency (0.67 vs 0.65 kg gain/kg feed intake; P &amp;lt; 0.05) compared to pigs fed control diets. Additionally, when pigs were provided OP throughout the nursery period (20 pens/treatment of 7 to 20 pigs/pen), average daily gain was increased 6.1% (0.48 vs 0.45 kg/d; P &amp;lt; 0.05), average daily feed intake tended to be increased 2.2% (0.62 vs 0.61 kg/d; P &amp;lt; 0.1), and feed efficiency was improved 2.7% (0.76 vs 0.74 kg gain/kg feed intake; P &amp;lt; 0.05) compared to pigs provided control diets. In conclusion, providing OP to pigs during the nursery period improved ADG and feed efficiency.
High-Throughput Recovery of Therapeutic Proteins from the Inclusion Bodies of <I>Escherichia coli</I>: An Overview (2005)

Escherichia coli is widely used for the expression of recombinant proteins that do not require glycosylation for their bioactivity (1,2). Many commercially available recombinant hormones and the majority of interleukins and interferons are all expressed and produced in E. coli systems (3). The advantages of using E. coli as an expression system include the enormous volume of data on its cell biology, its fermentation process development, and its ability to produce relatively large and inexpensive quantities of recombinant protein (4). However, the high-level expression of recombinant proteins in E. coli often results in the accumulation of the product as insoluble aggregates in vivo as inclusion bodies (5). Inclusion body proteins are devoid of biological activity and require elaborate solubilization and refolding procedures to recover functional activity (6,7). The renaturation of inclusion body proteins into a bioactive form is cumbersome, results in low recovery of the final product, and also accounts for the major cost in overall production of recombinant proteins using E. coli (7,8). However, whereas high-yielding processes are developed for the refolding of the aggregated recombinant proteins, high-level expression of proteins as inclusion bodies provides a straightforward strategy for producing therapeutic proteins. The initial high level of expression compensates for loss during recovery of the protein of interest from inclusion bodies. Despite many successful refolding procedures for inclusion body proteins (even at industrial scale), the renaturation process for each protein is quite different. Most often, this process is carried out in an empirical way and causes poor recovery of the bioactive therapeutic protein.
Correlation Between Corneal Biomechanical Indices and the Severity of Keratoconus (2019)

Corneal biomechanical indices correlated with corneal tomographic parameters in patients with KC. These findings support the possibility of developing biomechanical-based staging classification for KC in combination with topographic or tomographic indices.
Thermal/mechanical design and design automation for packaging (1999)

The need for mechanical and thermal analysis/synthesis is motivated through examples of applications. The development cycle for design is discussed in some detail and the criticality of comprehensive analysis to ensure successful design is discussed. It is demonstrated that successful integration of diverse functional and reliability requirements requires thorough studies of design options. The current state of the art in design synthesis and analysis tools is reviewed. It is suggested that design tools still need improvements in connectivity between electrical layout and thermal and mechanical analysis/synthesis tools. Another issue that needs greater emphasis is the issue of dimensional scale transitions in analyses at the die level vs those at the package and system levels. Both these issues are reviewed in context of the ability of current tools. Some challenges as we go forward are identified based on this review.
Combined Video-Assisted Thoracic Surgery and Posterior Spinal Surgery for the Treatment of Dumbbell Tumor of the First Thoracic Nerve Root (2015)

Although several cases of a dumbbell tumor of thoracic nerve roots have been reported, reports on the surgical procedures for a dumbbell tumor of the first thoracic (T1) nerve root are rare. Surgeons should be cautious, especially when performing a surgical procedure for a dumbbell tumor of the T1 nerve root because the tumor is anatomically located adjacent to important organs and because the T1 nerve root composes the lower trunk of the brachial plexus with the eighth cervical nerve root. We present cases with dumbbell tumors of the T1 nerve root that were treated with combined surgical treatment to remove the tumor. We first performed video-assisted thoracic surgery (VATS) to release the organs anteriorly and then performed posterior spinal surgery in the prone position. The combined VATS and posterior spinal surgery may become a standard surgical procedure for the treatment of dumbbell tumors of the T1 nerve root.
Virtual fences for controlling cows (2004)

We describe a moving virtual fence algorithm for herding cows. Each animal in the herd is given a smart collar consisting of a GPS, PDA, wireless networking and a sound amplifier. Using the GPS, the animal's location can be verified relative to the fence boundary. When approaching the perimeter, the animal is presented with a sound stimulus whose effect is to move away. We have developed the virtual fence control algorithm for moving a herd. We present simulation results and data from experiments with 8 cows equipped with smart collars.
Bone marrow from CD18-/- (MAC-1-/-) homozygous deletion recombinant negative mice demonstrates increased longevity in long-term bone marrow culture and decreased contribution to irradiation pulmonary damage. (2006)

The data demonstrate a complex role of CD18 (MAC-1) in macrophage progenitor and macrophage cellular interaction involving stromal cells of the bone marrow and lung.
Estimation and compensation of Doppler effect using variable sub-carrier spacing in multiband UAC OFDM systems (2010)

Doppler shift causes loss of orthogonality in Orthogonal Frequency Division Multiplexing (OFDM), which in turn may severely degrade receiver performance. In high data rate underwater acoustic communication (UAC), the effect of Doppler varies considerably over OFDM subcarriers. This paper will propose an algorithm to estimate the varying effects of Doppler shift over subcarriers and to avoid/mitigate the ICI produced by such effects using variable sub-carrier spacing in multiband OFDM.
Special regulatory T‐cell review: FOXP3 biochemistry in regulatory T cells – how diverse signals regulate suppression (2007)

FOXP3 is an acetylated and phosphorylated protein active in human regulatory T cells and forms oligomers which then associate with an even larger molecular complex. FOXP3 actively regulates transcription by recruiting enzymatic co-repressors and/or co-activators. FOXP3 complex ensembles are dynamically regulated by physiological stimuli such as T-cell receptor, IL-2 and proinflammation cytokine signals. Understanding the post-translational modifications of FOXP3 regulated by diverse signals and the biochemistry and structural chemistry of enzymatic proteins in the FOXP3 complex is critical for therapeutically modulating regulatory T cell function.
Safety and immunogenicity of 13-valent pneumococcal conjugate vaccine formulations with and without aluminum phosphate and comparison of the formulation of choice with 23-valent pneumococcal polysaccharide vaccine in elderly adults (2014)

This randomized open-label trial was designed to provide preliminary immunogenicity and safety data to support development of the pediatric 13-valent pneumococcal conjugate vaccine (PCV13) for adults. The aims were to: identify an age-appropriate PCV13 formulation, i.e., with (n = 309) or without (n = 304) aluminum phosphate (AlPO 4); compare the selected PCV13 formulation (n = 309) with 23-valent pneumococcal polysaccharide vaccine (PPSV23; n = 301); and, together with an extension study, assess sequential use of pneumococcal vaccines at 1-year intervals in adults aged ≥65 years (n = 105) not pre-vaccinated with PPSV23. Immune responses were measured by ELISA and opsonophagocytic activity assays 1 month postvaccination. Immunoglobulin G responses elicited by PCV13 with AlPO 4 and PCV13 without AlPO 4 were similar for the majority, and noninferior for all PCV13 serotypes. PCV13 with AlPO 4 was generally more reactogenic, with reactions mainly mild or moderate. Thus, PCV13 with AlPO 4 (hereafter PCV13) became the selected formulation. Immune responses to PCV13 were noninferior for all but one serotype and for most PCV13 serotypes superior to PPSV23. Vaccine sequence assessments showed that for PCV13/PPSV23, the initial PCV13 dose generally enhanced responses to a subsequent PPSV23 dose, compared with PPSV23 alone. For PCV13/PCV13, a second dose did not enhance the first dose response when given after 1 year. For PCV13/PPSV23/PCV13, priming with PCV13 (vaccination 1) did not protect against lower responses induced by PPSV23 to subsequent PCV13 (vaccination 3). In conclusion, the pediatric PCV13 formulation with AlPO 4 is well tolerated and immunogenic in adults, is generally more immunogenic than PPSV23, and subsequent vaccination with PPSV23 is possible if required.
Proteogenomics to probe non-model organisms and biodiversity (2015)

Advances in next-generation genome sequencing on one hand and high-throughput tandem mass spectrometry on the other have made proteomic experiments applicable to a vast range of organisms. Proteogenomics enables ambitious molecular studies starting from a genome draft or RNAseq data for establishing an exhaustive protein sequence database at a reasonable cost. While the proteomic methodologies are rather standard in these discovery-oriented experiments, interpretation of tandem mass spectrometry raw data remains difficult till now due to the size of the database to be considered and the quality of DNA sequencing and assembling which is far to be as confident as desirable. Besides, the confidence in functional annotation of new key proteins discovered in such experiments is directly linked to the density of closely-related species which have been sequenced and annotated so far. These general points will be exemplified with recent works done on extremophiles, such as the green algae Coccomyxa actinabiotis, and animals, such as the fresh water amphipode Gammarus fossarum. The latter cannot be cultivated as stable isolated specie in controlled laboratory conditions and thus, proteogenomic approaches are really challenging for such sample. Despite these difficulties, the biological impact of different xenobiotics on testis of G. fossarum males could be monitored by high-throughput proteomics. We could also define the core-proteome of the female reproductive organ and explore its conservation throughout different Gammarids. The large molecular biodiversity of Life on Earth is another level of complexity, but as shown with Gammarids, comparative proteogenomics could become more preeminent in evolutionary biology.
Long Term Follow‐up Data and Health‐Related Quality of Life in Frontline Therapy of Fit Patients Treated With FCR Versus BR (CLL10 Trial of the GCLLSG) (2020)

Fludarabine, cyclophosphamide and rituximab (FCR) was compared to bendamustine and rituximab (BR) in an international, randomized, open label, phase 3 trial in 561 previously untreated, fit patients with chronic lymphocytic leukemia (CLL) without del (17p). Primary endpoint was progression free survival (PFS). The final primary endpoint analysis after 37.1 months median follow up failed to show the non-inferiority of BR as compared with FCR. With extended median follow up of 58.2 months, median PFS was 42.3 months in BR-treated patients versus 57.6 months for FCR-treated patients (Hazard Ratio [HR] 1.593; 95% CI 1.271-1.996; p < 0.0001). For patients > 65 years, median PFS was 48.5 months with BR versus 57.9 months with FCR without reaching statistical significance (HR 1.352; 95% CI 0.912-2.006; p = 0.134). Median OS was not reached for both arms with 5-year OS rates of 80.1% vs 80.9%, respectively (HR 1.108; 95% CI 0.755-1.627; p = 0.599). No statistically significant difference was found in the time to secondary malignancy between the 2 groups (at 5 years, 86.6% free from secondary malignancies in the BR group vs 83.8% in the FCR group [HR 0.801; 95% CI 0.507-1.267; p = 0.344]). In patients >65 years secondary neoplasia occurred more frequently after FCR treatment [28 of 86 (32.6%) patients] as compared with BR [18 of 107 (16.8%) patients; p = 0.011]. Health-related quality of life was similar in both treatments. Despite the improved PFS for FCR, OS did not differ. These results also suggest an increase in secondary neoplasia associated with FCR in elderly fit CLL patients.
Chemical Passivation of Silicon Nanowires with C1−C6 Alkyl Chains through Covalent Si−C Bonds (2008)

We report on the functionalization of Si NWs with C1−C6 alkyl chains using a versatile two step chlorination/alkylation process. We show that Si NWs terminated with C1−C6 molecules, through Si−C bonds, connect alkyl molecules to 50−100% of the Si atop sites and provide surface stability that depends on the chain length and molecular coverage, according to the following order: C1−Si NW > C2−Si NW > (C3−C6)−Si NW. Our results indicate that the oxidation resistance of (C1−C2)−Si NWs is significantly higher than equivalent 2D Si(100) surfaces, whereas (C3−C6)−Si NWs are comparable to 2D (C3−C6)−Si(100). These discrepancies can be explained as follows: the lower the molecular coverage, the higher the probability for interaction between oxidizing agents (O2 or H2O) and molecule-free sites. Our results are of practical importance when reduced amounts of oxide are required, e.g., for radial epitaxy on NWs to realize vertical P−N junctions for solar cells or for radial Si/Ge superlattices for application in optoelectronics.
Impacts of strained SiO/sub 2/ on TDDB lifetime projection (2002)

We clarify the effects of the strained-SiO/sub 2/ on the time dependent dielectric breakdown (TDDB) characteristics, the activation energy of the oxide breakdown and Weibull slope (/spl beta/) for the ultra-thin gate oxide. Considerations based on the extended-Stillinger-Weber potential model show that the built-in compressive strain in SiO/sub 2/ changes the statistical distribution of the Si-O-Si angle, leading to a decrease of T/sub pd/ and a spread of the distribution. The oxide breakdown tends to occur at the Si-O-Si network with a lower bond angle (/spl sim/115/spl deg/) for the 2 nm-thick SiO/sub 2//Si system.
Control of MEMS on the edge of instability (2011)

This paper investigates a new method for tracking parameters at which dynamic bifurcations occur in MEMS based on state statistics of a resonator. Experimental results show that observed changes in phase and amplitude precede a sub-critical pitchfork bifurcation. Feedback control, based on the statistics of the phase, is then employed to stabilize a device on the edge of instability. Sensitivity to changes in device parameters is explored and initial results show high sensitivity is obtained for low vibration amplitudes. Furthermore, experimental results on the same device using an older method of bifurcation sensing show acquisition rate improvement by over three orders of magnitude with the new method.
A distributed algorithm for adaptive traffic lights control (2012)

In this paper, we address the problem of controlling traffic lights at an intersection with a spatially distributed sensor network. We propose a sensor network architecture that does not depend on a centralized coordinator and we separate logically it into 4 levels of hierarchy. On this architecture, we define and evaluate through simulations an adaptive traffic light control algorithm. Based on two main objectives, this algorithm decides dynamically of the green lights sequences by selecting the movements composing each phase and its duration. Simulation results show that this algorithm, if properly tuned, has the capacity to reduce average waiting time at an intersection, while avoiding starvation.
Immune Gene Networks of Mycobacterial Vaccine–Elicited Cellular Responses and Immunity (2006)

Gene networks of protective lymphocytes after immune activation with live attenuated vaccines remain poorly characterized. Because Mycobacterium bovis bacille Calmette-Guérin (BCG) vaccine can confer protection against fatal forms of tuberculosis in humans and monkeys, we made use of macaque models to optimally study immune gene networks after BCG vaccination/infection. We first established and validated a large-scale real-time quantitation system and then used it to measure expression levels of 138 immune genes after BCG vaccination/infection of rhesus macaques. Systemic BCG vaccination induced up to 600-fold increases in expression of 78 immune genes among the 138 genes tested at the time when BCG-elicited T cell responses and immunity were apparent. These up-regulated transcripts constituted multiple gene networks that were linked to various aspects of immune function. Surprisingly, the up-regulation of most of these immune genes in the gene networks occurred at 1 week and was sustained at > or = 6 weeks after BCG vaccination/infection. Although early activation of immune gene networks was an immune correlate of anti-BCG immunity, prolonged up-regulation of these networks coincided with the development of vaccine-elicited T cell responses after BCG vaccination/infection. These findings provide molecular evidence suggesting that the BCG-induced gene networks may represent global transcriptomes and proteomes underlying the development of T cell responses and, ultimately, immunity to mycobacteria.
Application of convolutional artificial neural networks to echocardiograms for differentiating congenital heart diseases in a pediatric population (2017)

In this paper we describe a pilot study, where machine learning methods are used to differentiate between congenital heart diseases. Our approach was to apply convolutional neural networks (CNNs) to echocardiographic images from five different pediatric populations: normal, coarctation of the aorta (CoA), hypoplastic left heart syndrome (HLHS), transposition of the great arteries (TGA), and single ventricle (SV). We used a single network topology that was trained in a pairwise fashion in order to evaluate the potential to differentiate between patient populations. In total we used 59,151 echo frames drawn from 1,666 clinical sequences. Approximately 80% of the data was used for training, and the remainder for validation. Data was split at sequence boundaries to avoid having related images in the training and validation sets. While training was done with echo images/frames, evaluation was performed for both single frame discrimination as well as sequence discrimination (by majority voting). In total 10 networks were generated and evaluated. Unlike other domains where this network topology has been used, in ultrasound there is low visual variation between classes. This work shows the potential for CNNs to be applied to this low-variation domain of medical imaging for disease discrimination.