gebhart/patrepeval huggingface dataset:
Reinforcement learning for bandwidth estimation and congestion control in real-time communications (2019)

Bandwidth estimation and congestion control for real-time communications (i.e., audio and video conferencing) remains a difficult problem, despite many years of research. Achieving high quality of experience (QoE) for end users requires continual updates due to changing network architectures and technologies. In this paper, we apply reinforcement learning for the first time to the problem of real-time communications (RTC), where we seek to optimize user-perceived quality. We present initial proof-of-concept results, where we learn an agent to control sending rate in an RTC system, evaluating using both network simulation and real Internet video calls. We discuss the challenges we observed, particularly in designing realistic reward functions that reflect QoE, and in bridging the gap between the training environment and real-world networks.
Pitolisant, a wake‐promoting agent devoid of psychostimulant properties: Preclinical comparison with amphetamine, modafinil, and solriamfetol (2021)

Several therapeutic options are currently available to treat excessive daytime sleepiness (EDS) in patients suffering from narcolepsy or obstructive sleep apnea. However, there are no comparisons between the various wake-promoting agents in terms of mechanism of action, efficacy, or safety. The goal of this study was to compare amphetamine, modafinil, solriamfetol, and pitolisant at their known primary pharmacological targets, histamine H3 receptors (H3R), dopamine, norepinephrine, and serotonin transporters, and in various in vivo preclinical models in relation to neurochemistry, locomotion, behavioral sensitization, and food intake. Results confirmed that the primary pharmacological effect of amphetamine, modafinil, and solriamfetol was to increase central dopamine neurotransmission, in part by inhibiting its transporter. Furthermore, solriamfetol increased levels of extracellular dopamine in the nucleus accumbens, and decreased the 3,4-dihydroxyphenyl acetic acid (DOPAC)/DA ratio in the striatum, as reported for modafinil and amphetamine. All these compounds produced hyperlocomotion, behavioral sensitization, and hypophagia, which are common features of psychostimulants and of compounds with abuse potential. In contrast, pitolisant, a selective and potent H3R antagonist/inverse agonist that promotes wakefulness, had no effect on striatal dopamine, locomotion, or food intake. In addition, pitolisant, devoid of behavioral sensitization by itself, attenuated the hyperlocomotion induced by either modafinil or solriamfetol. Therefore, pitolisant presents biochemical, neurochemical, and behavioral profiles different from those of amphetamine and other psychostimulants such as modafinil or solriamfetol. In conclusion, pitolisant is a differentiated therapeutic option, when compared with psychostimulants, for the treatment of EDS, as this agent does not show any amphetamine-like properties within in vivo preclinical models.
Variant Forms of α-Fetoprotein Transcripts Expressed in Human Hematopoietic Progenitors (2002)

Hematopoietic stem cells have been identified as multipotent cells that give rise to all adult hematopoietic lineages. Although the hematopoietic lineage is derived from the mesodermal germ layer in the embryo, recent data suggest that bone marrow cells with an antigenic profile consistent with that of hematopoietic stem cells can also differentiate to cell types of the endodermal lineages, such as hepatocytes. However, the molecular mechanisms associated with these events are entirely unknown. For decades, alpha-fetoprotein (AFP) has been used as a differentiation marker for endodermal cells, because it was thought that the transcription of AFP mRNA is tightly regulated in a developmental and tissue-specific process. In this report we describe two new variant forms of AFP transcripts in human hematopoietic progenitors that are not expressed in mature cells. The variant AFP (vAFP) cDNA sequences isolated from a multipotent hematopoietic cell line, K562, revealed that the vAFP differed from the authentic transcript, consisting of 15 exons, by replacing exon 1 of AFP with one or two exons located in the 5'-untranslated region of the AFP gene. In addition to the K562 cell line, vAFP transcripts were detected in normal bone marrow, thymus, and brain but were not detected in normal spleen, intestine, liver, or the hepatocellular carcinoma cell line, HepG2. This suggests expression in normal hematopoietic progenitors. This hypothesis was confirmed by the finding that CD34(+)Lin(-) hematopoietic progenitor cells purified from cord blood by flow cytometric sorting also expressed the variant transcripts. These results suggest that some hematopoietic progenitors are in a state that permits them to express certain types of transcripts that have been considered unique to endoderm.
Split-spectrum phase-gradient optical coherence tomography angiography (2016)

A phase gradient angiography (PGA) method is proposed for optical coherence tomography (OCT). This method allows the use of phase information to map the microvasculature in tissue without the correction of bulk motion and laser trigger jitter induced phase artifacts. PGA can also be combined with the amplitude/intensity to improve the performance. Split-spectrum technique can further increase the signal to noise ratio by more than two times. In-vivo imaging of human retinal circulation is shown with a 70 kHz, 840 nm spectral domain OCT system and a 200 kHz, 1050 nm swept source OCT system. Four different OCT angiography methods are compared. The best performance was achieved with split-spectrum amplitude and phase-gradient angiography.
A New Production Process of Organic Pigment Nanocrystals (2008)

By using the reprecipitation method known as an organic nanocrystal preparation method, the preparation of organic pigment nanocrystals with a particle size of about 25 nm was easily achievable. When they were used for the color filter of liquid crystal displays, clear improvement in the contrast ratio was confirmed.
Electron density dependence of impedance probe plasma potential measurements (2015)

In earlier works, we used spheres of various sizes as impedance probes in demonstrating a method of determining plasma potential, φp, when the probe radius is much larger than the Debye length, λD. The basis of the method in those works [Walker et al., Phys. Plasmas 13, 032108 (2006); ibid. 15, 123506 (2008); ibid. 17, 113503 (2010)] relies on applying a small amplitude signal of fixed frequency to a probe in a plasma and, through network analyzer-based measurements, determining the complex reflection coefficient, Γ, for varying probe bias, Vb. The frequency range of the applied signal is restricted to avoid sheath resonant effects and ion contributions such that ωpi ≪ ω ≪ ωpe, where ωpi is the ion plasma frequency and ωpe is the electron plasma frequency. For a given frequency and applied bias, both Re(Zac) and Im(Zac) are available from Γ. When Re(Zac) is plotted versus Vb, a minimum predicted by theory occurs at φp [Walker et al., Phys. Plasmas 17, 113503 (2010)]. In addition, Im(Zac) appears at, or very near, a maximum at φp. As ne decreases and the sheath expands, the minimum becomes harder to discern. The purpose of this work is to demonstrate that when using network analyzer-based measurements, Γ itself and Im(Zac) and their derivatives are useful as accompanying indicators to Re(Zac) in these difficult cases. We note the difficulties encountered by the most commonly used plasma diagnostic, the Langmuir probe. Spherical probe data is mainly used in this work, although we present limited data for a cylinder and a disk. To demonstrate the effect of lowered density as a function of probe geometry, we compare the cylinder and disk using only the indicator Re(Zac).
Identification and elimination of an immunodominant T-cell epitope in recombinant immunotoxins based on<i>Pseudomonas</i>exotoxin A (2012)

Recombinant immunotoxins (RITs) are chimeric proteins that are being developed for cancer treatment. We have produced RITs that contain PE38, a portion of the bacterial protein Pseudomonas exotoxin A. Because the toxin is bacterial, it often induces neutralizing antibodies, which limit the number of treatment cycles and the effectiveness of the therapy. Because T cells are essential for antibody responses to proteins, we adopted an assay to map the CD4(+) T-cell epitopes in PE38. We incubated peripheral blood mononuclear cells with an immunotoxin to stimulate T-cell expansion, followed by exposure to overlapping peptide fragments of PE38 and an IL-2 ELISpot assay to measure responses. Our observation of T-cell responses in 50 of 50 individuals correlates with the frequency of antibody formation in patients with normal immune systems. We found a single, highly immunodominant epitope in 46% (23/50) of the donors. The immunodominant epitope is DRB1-restricted and was observed in subjects with different HLA alleles, indicating promiscuity. We identified two amino acids that, when deleted or mutated to alanine, eliminated the immunodominant epitope, and we used this information to construct mutant RITs that are highly cytotoxic and do not stimulate T-cell responses in many donors.
Prognostic DNA Methylation Markers for Prostate Cancer (2014)

Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC.
A Method to Improve Reliability in a 65-nm SRAM PUF Array (2018)

A modified weak SRAM physical unclonable function (PUF) is proposed which is much more reliable than prior-art SRAM PUFs. The proposed PUF was fabricated in TSMC 65-nm process. A novel preselection test was run on these PUF arrays and is shown to eliminate all of the unstable cells (20%-25%). This PUF can drastically reduce the need for error correction codes. In addition, the preselection test can be accomplished in one VDD/temperature corner, which reduces the testing cost of finding unstable bits across many such corners, as is done in the prior art.
Hepatitis A virus, TIM-1 and allergy (2009)

In 1989, Strachan first proposed the hygiene hypothesis to explain the rapid increase in the prevalence of allergy and asthma. While the significant rise in the prevalence of asthma and allergy remains unexplained, epidemiological data suggest that infection with the Hepatitis A virus (HAV) might protect against asthma and allergy, and genetic studies identifying the HAV receptor, TIM-1, as an important atopy susceptibility gene, support this idea. In this chapter, we review the genetics and immunobiology of TIM-1 and TIM gene family members, and the possibility that HAV and TIM-1 may regulate the development of asthma and allergy.
Genetic and epigenetic properties of mouse male germline stem cells during long-term culture (2005)

Although stem cells are believed to divide infinitely by self-renewal division, there is little evidence that demonstrates their infinite replicative potential. Spermatogonial stem cells are the founder cell population for spermatogenesis. Recently, in vitro culture of spermatogonial stem cells was described. Spermatogonial stem cells can be expanded in vitro in the presence of glial cell line-derived neurotrophic factor (GDNF), maintaining the capacity to produce spermatogenesis after transplantation into testis. Here, we examined the stability and proliferative capacity of spermatogonial stem cells using cultured cells. Spermatogonial stem cells were cultured over 2 years and achieved approximately 10(85)-fold expansion. Unlike other germline cells that often acquire genetic and epigenetic changes in vitro, spermatogonial stem cells retained the euploid karyotype and androgenetic imprint during the 2-year experimental period, and produced normal spermatogenesis and fertile offspring. However, the telomeres in spermatogonial stem cells gradually shortened during culture, suggesting that they are not immortal. Nevertheless, the remarkable stability and proliferative potential of spermatogonial stem cells suggest that they have a unique machinery to prevent transmission of genetic and epigenetic damages to the offspring, and these characteristics make them an attractive target for germline modification.
Scalable Java Communication Middleware for Hybrid Shared/Distributed Memory Architectures (2011)

The up trend in the number of cores in cluster architectures underscores the need for scalable communication middleware on these systems. One of the strategies to take advantage of this increase in the available computational power is the use of efficient message-passing middleware for inter-node communications and thread-based shared memory transfers within each node. This paper presents a Java communication middleware that exploits hybrid shared/distributed memory architectures through the use of scalable Java NIO sockets for inter-node communications and multi-threading on shared memory. Thus, communication-intensive applications running on clusters of multi-core processors can take advantage of the use of this middleware. The performance of these codes generally relies on collective operations, such as broadcasting, scattering or gathering data, which have been optimized to make the most of these architectures. The evaluation of this middleware when relying on multi-core aware communication patterns has shown significant performance improvements both in collective operations and communication-intensive applications.
The Qx-coder (1998)

The IBM Adaptive Bilevel Image Compression (ABIC) algorithm depends upon the hardware-optimized Q-coder. The Joint Bi-level Image Experts Group (JBIG) settled upon a software-optimized QM-coder. This paper explores the incompatibilities of the hardware- and software-optimized binary arithmetic coding conventions and reports on the solution that allowed a merged Qx-coder in hardware. A unique hardware solution is presented for the termination of the JBIG data stream (CLEARBITS). The probability estimation is presented in a common format. Detailed flowcharts are included in the Appendix. An ASIC core is available that supports both the ABIC and JBIG bilevel data compression standards using this merged Qx-coder.
A Three-Dimensional Reservoir, Wellbore, and Hydraulic Fracturing Simulator that is Compositional and Thermal, Tracks Proppant and Water Solute Transport, Includes Non-Darcy and Non-Newtonian Flow, and Handles Fracture Closure (2017)

Abstract We present a three-dimensional reservoir, wellbore, and hydraulic fracturing simulator with the following capabilities: (1) compositional fluid model, (2) multiphase flow, (3) thermal, (4) proppant transport with gravitational settling, bulk slurry gravitational convection, hindered settling, clustered settling, and the effect of proppant concentration on slurry viscosity, (5) solute transport, (6) non-Newtonian fluid rheology with the modified power law (capable of representing the low shear rate viscosity plateau), (7) non-Darcy flow in the fractures, and (8) the ability to handle fracture closure. The simulator is still a work-in-progress; additional features are planned in future work. The simulator is a practical tool for designing hydraulic fracturing treatments and predicting future production. The combination of reservoir and fracturing simulation enables: (1) comparison of proposed frac designs on the basis of predicted production, (2) more realistic simulation of pressure drawdown in the fracture during production by using flow equations designed for fracture flow, (3) description of processes involving tight coupling of production and stimulation, such as refracturing, and (4) avoidance of tedious handoffs between separate fracturing and reservoir simulation codes. We develop general-purpose constitutive equations for fracture transport that are realistic for mechanically open or closed fractures and for all values of proppant mass per fracture area. In limiting cases, the equations reduce to well-known constitutive equations, such as Darcy's law, the cubic law, and Forchheimer's law. Between limiting cases, the equations smoothly transition between governing regimes. The current model is applicable for hydraulic fracturing in formations that do not exhibit strong fracture network "complexity" during stimulation. Modeling stimulation of secondary fractures requires special considerations that are not implemented in the current version of the code. We demonstrate the model capabilities with a generic simulation of a single-stage frac job from a vertical well, followed by production. After the injection of a pad, water is injected with 60 mesh proppant. This is followed by lower rate injection of water gelled with guar and 20 mesh proppant. The fracturing treatment generates a large, well-propped fracture. The fracture propagates below the water-hydrocarbon contact, resulting in significant watercut during production.
Making Polymeric Microspheres (1989)

Combination of advanced techniques yields uniform particles for biomedical applications. Process combines ink-jet and irradiation/freeze-polymerization techniques to make polymeric microspheres of uniform size in diameters from 100 to 400 micrometer. Microspheres used in chromatography, cell sorting, cell labeling, and manufacture of pharmaceutical materials.
The Secreted Effector Protein EspZ Is Essential for Virulence of Rabbit Enteropathogenic Escherichia coli (2015)

Attaching and effacing (A/E) pathogens adhere intimately to intestinal enterocytes and efface brush border microvilli. A key virulence strategy of A/E pathogens is the type III secretion system (T3SS)-mediated delivery of effector proteins into host cells. The secreted protein EspZ is postulated to promote enterocyte survival by regulating the T3SS and/or by modulating epithelial signaling pathways. To explore the role of EspZ in A/E pathogen virulence, we generated an isogenic espZ deletion strain (ΔespZ) and corresponding cis-complemented derivatives of rabbit enteropathogenic Escherichia coli and compared their abilities to regulate the T3SS and influence host cell survival in vitro. For virulence studies, rabbits infected with these strains were monitored for bacterial colonization, clinical signs, and intestinal tissue alterations. Consistent with data from previous reports, espZ-transfected epithelial cells were refractory to infection-dependent effector translocation. Also, the ΔespZ strain induced greater host cell death than did the parent and complemented strains. In rabbit infections, fecal ΔespZ strain levels were 10-fold lower than those of the parent strain at 1 day postinfection, while the complemented strain was recovered at intermediate levels. In contrast to the parent and complemented mutants, ΔespZ mutant fecal carriage progressively decreased on subsequent days. ΔespZ mutant-infected animals gained weight steadily over the infection period, failed to show characteristic disease symptoms, and displayed minimal infection-induced histological alterations. Terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) staining of intestinal sections revealed increased epithelial cell apoptosis on day 1 after infection with the ΔespZ strain compared to animals infected with the parent or complemented strains. Thus, EspZ-dependent host cell cytoprotection likely prevents epithelial cell death and sloughing and thereby promotes bacterial colonization.
Polarization field engineering with Type-II InGaN-GaNAs quantum well for improved nitride gain media at 420&#x2013;550 nm (2006)

Novel type-II InGaN-GaNAs quantum well is presented and analyzed as improved gain media for efficient light emitting diodes and laser diodes emitting at 420-nm up to 550-nm, with a large electronhole wavefunction overlap (Γ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e_hh</inf> ≫65–70%).
Evading pre-existing anti-hinge antibody binding by hinge engineering (2016)

Antigen-binding fragments (Fab) and F(ab')<sub>2</sub> antibodies serve as alternative formats to full-length anti-bodies in therapeutic and immune assays. They provide the advantage of small size, short serum half-life, and lack of effector function. Several proteases associated with invasive diseases are known to cleave antibodies in the hinge-region, and this results in anti-hinge antibodies (AHA) toward the neoepitopes. The AHA can act as surrogate Fc and reintroduce the properties of the Fc that are otherwise lacking in antibody fragments. While this response is desired during the natural process of fighting disease, it is commonly unwanted for therapeutic antibody fragments. In our study, we identify a truncation in the lower hinge region of the antibody that maintains efficient proteolytic cleavage by IdeS protease. The resulting neoepitope at the F(ab')<sub>2</sub> C-terminus does not have detectable binding of pre-existing AHA, providing a practical route to produce F(ab')<sub>2</sub> in vitro by proteolytic digestion when the binding of pre-existing AHA is undesired. We extend our studies to the upper hinge region of the antibody and provide a detailed analysis of the contribution of C-terminal residues of the upper hinge of human IgG1, IgG2 and IgG4 to pre-existing AHA reactivity in human serum. While no pre-existing antibodies are observed toward the Fab of IgG2 and IgG4 isotype, a significant response is observed toward most residues of the upper hinge of human IgG1. We identify a T<sub>225</sub>L variant and the natural C-terminal D<sub>221</sub> as solutions with minimal serum reactivity. Our work now enables the production of Fab and F(ab')<sub>2</sub> for therapeutic and diagnostic immune assays that have minimal reactivity toward pre-existing AHA.