gebhart/patrepeval huggingface dataset:
Data from A Phase II, Randomized, Open-Label Study of Neoadjuvant Degarelix versus LHRH Agonist in Prostate Cancer Patients Prior to Radical Prostatectomy (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Degarelix, a new gonadotropin-releasing hormone (GnRH) receptor antagonist with demonstrated efficacy as first-line treatment in the management of high-risk prostate cancer, possesses some theoretical advantages over luteinizing hormone–releasing hormone (LHRH) analogues in terms of avoiding “testosterone flare” and lower follicle-stimulating hormone (FSH) levels. We set out to determine whether preoperative degarelix influenced surrogates of disease control in a randomized phase II study.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Thirty-nine patients were randomly assigned to one of three different neoadjuvant arms: degarelix only, degarelix/bicalutamide, or LHRH agonist/bicalutamide. Treatments were given for 3 months before prostatectomy. Patients had localized prostate cancer and had chosen radical prostatectomy as primary treatment. The primary end point was treatment effect on intratumoral dihydrotestosterone levels.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Intratumoral DHT levels were higher in the degarelix arm than both the degarelix/bicalutamide and LHRH agonist/bicalutamide arms (0.87 ng/g vs. 0.26 ng/g and 0.23 ng/g, &lt;i&gt;P&lt;/i&gt; &lt; 0.01). No significant differences existed for other intratumoral androgens, such as testosterone and dehydroepiandrosterone. Patients in the degarelix-only arm had higher AMACR levels on immunohistochemical analysis (&lt;i&gt;P&lt;/i&gt; = 0.01). Serum FSH levels were lower after 12 weeks of therapy in both degarelix arms than the LHRH agonist/bicalutamide arm (0.55 and 0.65 vs. 3.65, &lt;i&gt;P&lt;/i&gt; &lt; 0.01), and inhibin B levels were lower in the degarelix/bicalutamide arm than the LHRH agonist/bicalutamide arm (82.14 vs. 126.67, &lt;i&gt;P&lt;/i&gt; = 0.02).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Neoadjuvant degarelix alone, compared with use of LHRH agonist and bicalutamide, is associated with higher levels of intratumoral dihydrotestosterone, despite similar testosterone levels. Further studies that evaluate the mechanisms behind these results are needed. &lt;i&gt;Clin Cancer Res; 23(8); 1974–80. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Transient and selectable transformation of the parasitic protist  Trichomonas vaginalis (1997)

We have developed methods to transiently and selectably transform the human-infective protist Trichomonas vaginalis. This parasite, a common cause of vaginitis worldwide, is one of the earlier branching eukaryotes studied to date. We have introduced three heterologous genes into T. vaginalis by electroporation and have used the 5' and 3' untranslated regions of the endogenous gene alpha-succinyl CoA synthetase B (alpha-SCSB) to drive transcription of these genes. Transient expression of two reporter proteins, chloramphenicol acetyltransferase (CAT) or luciferase, was detected when electroporating in the presence of 50 microg closed-circular construct. Optimal levels of expression were observed using approximately 2.5 x 10(8) T. vaginalis cells and 350 volts, 960 microFd for electroporation; however, other conditions also led to significant reporter gene expression. A time course following the expression of CAT in T. vaginalis transient transformants revealed the highest level of expression 8-21 hr postelectroporation and showed that CAT activity is undetectable using TLC by 99 hr postelectroporation. The system we established to obtain selectable transformants uses the neomycin phosphotransferase (neo) gene as the selectable marker. Cells electroporated with 20 microg of the NEO construct were plated in the presence of 50 microg/ml paromomycin and incubated in an anaerobic chamber. The paromomycin-resistant colonies that formed within 3-5 days were cultivated in the presence of drug and DNA was isolated for analyses. The NEO construct was shown to be maintained episomally, as a closed-circle, at between 10-30 copies per cell. The ability to transiently and selectably transform T. vaginalis should greatly enhance research on this important human parasite.
Digitally Optimized Delta-Sigma Modulator for WiMAX Transmitter Design (2007)

This paper proposes a new approach to reduce the sampling rate in delta-sigma (DeltaSigma) transmitters and, hence, to lower considerably the speed requirements of all critical digital circuit blocks. The proposed method relies on oversampling the signal by inserting zeros after the low-pass DeltaSigma-modulation and to use one of the harmonic outputs of the sampler instead of its fundamental. The optimum sampling frequency in terms of signal integrity and out-of-band performance is determined for this configuration through simulations. Using a sampling frequency of only 288 MHz, EVM and ACPR for a WiMAX signal with a bandwidth of 2 MHz around 2.45 GHz are 7 % and -55 dBc, respectively
The Nontypeable Haemophilus influenzae Major Adhesin Hia Is a Dual-Function Lectin That Binds to Human-Specific Respiratory Tract Sialic Acid Glycan Receptors (2020)

NTHi is a human-adapted pathogen that colonizes the human respiratory tract. Strains of NTHi express multiple adhesins; however, there is a unique, mutually exclusive relationship between the major adhesins Hia and HMW1 and HMW2 (HMW1/2). Approximately 25% of NTHi strains express Hia, a phase-variable autotransporter protein that has a critical role in colonization of the host nasopharynx. The remaining 75% of strains express HMW1/2. Previous work has shown that the HMW1 and HMW2 proteins mediate binding to 2-3- and 2-6-linked sialic acid glycans found in the human respiratory tract. Here, we show that the high-affinity binding domain of Hia, binding domain 1 (BD1), is responsible for binding to α2-6-sialyllactosamine (2-6 SLN) glycans. BD1 is highly specific for glycans that incorporate the form of sialic acid expressed by humans, <i>N</i>-acetylneuraminic acid (Neu5Ac). We further show that Hia has lower-affinity binding activity for 2-3-linked sialic acid and that this binding activity is mediated via a distinct domain. Thus, Hia with its dual binding activities functionally mimics the combined activities of the HMW1 and HMW2 adhesins. In addition, we show that Hia has a role in biofilm formation by strains of NTHi that express the adhesin. Knowledge of the binding affinity of this major NTHi adhesin and putative vaccine candidate will direct and inform development of future vaccines and therapeutic strategies for this important pathogen.<b>IMPORTANCE</b> Host-adapted bacterial pathogens like NTHi have evolved specific mechanisms to colonize their restricted host niche. Relatively few of the adhesins expressed by NTHi have been characterized as regards their binding affinity at the molecular level. In this work, we show that the major NTHi adhesin Hia preferentially binds to Neu5Ac-α2-6-sialyllactosamine, the form of sialic acid expressed in humans. The receptors targeted by Hia in the human airway mirror those targeted by influenza A virus and indicates the broad importance of sialic acid glycans as receptors for microbes that colonize the human airway.
[Actual situations and problems of patients receiving home IVH--trial use of an assessment chart for outpatients]. (1999)

In order to improve the quality of life (QOL) and continue nursing, we used an assessment chart to investigate the actual situations and problems of the patients receiving home intravenous hyperalimentation (IVH). From January, 1997 to June, 1999, we investigated 20 patients with home IVH. To 7 patients among them, we asked questions using Kurihara's assessment chart for QOL, plus our original questions concerning IVH. The mean age of the patients was 61 years old, and 19 of them had advanced cancers. Forty percent of the patients maintained the IVH all by themselves and 10% of the patients needed the support of their family. The remaining 50% of the patients left all to their family. There were 9 incidents of trouble during the maintenance of the IVH. Almost all patients from whom informed consent had been received were satisfied with the home IVH. On the contrary, all patients who had not given informed consent were not satisfied with the home IVH. According to the results of the assessment chart, even if the total points were low, the points for the IVH were high in the patients had given informed consent. The main reason for lower QOL was pain. The points for the families were lower than those for the patients. They sometimes complained of uneasiness and dissatisfaction with the support they received. We conclude that therapies to improve symptoms and mental state are necessary to satisfy the patients, and that it is important to support not only the patients but also their families.
Efficient frequent item counting in multi-core hardware (2012)

The increasing number of cores and the rich instruction sets of modern hardware are opening up new opportunities for optimizing many traditional data mining tasks. In this paper we demonstrate how to speed up the performance of the computation of frequent items by almost one order of magnitude over the best published results by matching the algorithm to the underlying hardware architecture.
‘North Sea’ progressive myoclonus epilepsy: phenotype of subjects with GOSR2 mutation (2013)

We previously identified a homozygous mutation in the Golgi SNAP receptor complex 2 gene (GOSR2) in six patients with progressive myoclonus epilepsy. To define the syndrome better we analysed the clinical and electrophysiological phenotype in 12 patients with GOSR2 mutations, including six new unrelated subjects. Clinical presentation was remarkably similar with early onset ataxia (average 2 years of age), followed by myoclonic seizures at the average age of 6.5 years. Patients developed multiple seizure types, including generalized tonic clonic seizures, absence seizures and drop attacks. All patients developed scoliosis by adolescence, making this an important diagnostic clue. Additional skeletal deformities were present, including pes cavus in four patients and syndactyly in two patients. All patients had elevated serum creatine kinase levels (median 734 IU) in the context of normal muscle biopsies. Electroencephalography revealed pronounced generalized spike and wave discharges with a posterior predominance and photosensitivity in all patients, with focal EEG features seen in seven patients. The disease course showed a relentless decline; patients uniformly became wheelchair bound (mean age 13 years) and four had died during their third or early fourth decade. All 12 cases had the same variant (c.430G>T, G144W) and haplotype analyses confirmed a founder effect. The cases all came from countries bounding the North Sea, extending to the coastal region of Northern Norway. 'North Sea' progressive myoclonus epilepsy has a homogeneous clinical presentation and relentless disease course allowing ready identification from the other progressive myoclonus epilepsies.
Mitochondrial Reactive Oxygen Species Generated at the Complex-II Matrix or Intermembrane Space Microdomain Have Distinct Effects on Redox Signaling and Stress Sensitivity in Caenorhabditis elegans (2019)

<b><i>Aims:</i></b> How mitochondrial reactive oxygen species (ROS) impact physiological function may depend on the quantity of ROS generated or removed, and the subcellular microdomain in which this occurs. However, pharmacological tools currently available to alter ROS production <i>in vivo</i> lack precise spatial and temporal control. <b><i>Results:</i></b> We used CRISPR/Cas9 to fuse the light-sensitive ROS-generating protein, SuperNova to the C-terminus of mitochondrial complex II succinate dehydrogenase subunits B (SDHB-1::SuperNova) and C (SDHC-1::SuperNova) in <i>Caenorhabditis elegans</i> to localize SuperNova to the matrix-side of the inner mitochondrial membrane, and to the intermembrane space (IMS), respectively. The presence of the SuperNova protein did not impact complex II activity, mitochondrial respiration, or <i>C. elegans</i> development rate under dark conditions. ROS production by SuperNova protein <i>in vitro</i> in the form of superoxide (O<sub>2</sub>˙<sup>-</sup>) was both specific and proportional to total light irradiance in the 540-590 nm spectra, and was unaffected by varying the buffer pH to resemble the mitochondrial matrix or IMS environments. We then determined using SuperNova whether stoichiometric ROS generation in the mitochondrial matrix or IMS had distinct effects on redox signaling <i>in vivo</i>. Phosphorylation of PMK-1 (a p38 MAPK homolog) and transcriptional activity of SKN-1 (an Nrf2 homolog) were each dependent on both the site and duration of ROS production, with matrix-generated ROS having more prominent effects. Furthermore, matrix- but not IMS-generated ROS attenuated susceptibility to simulated ischemia reperfusion injury in <i>C. elegans</i>. <b><i>Innovation and Conclusion:</i></b> Overall, these data demonstrate that the physiological output of ROS depends on the microdomain in which it is produced. <i>Antioxid. Redox Signal.</i> 31, 594-607.
Specific CD4 down-modulating compounds with potent anti-HIV activity (2003)

Despite the availability of the current clinically approved anti-HIV drugs, new classes of effective antiviral agents are still urgently needed to combat AIDS. A promising approach for drug development and vaccine design involves targeting research on HIV-1 entry, a multistep process that comprises viral attachment, coreceptor interactions, and fusion. Determination of the viral entry process in detail has enabled the design of specific agents that can inhibit each step in the HIV entry process. Therapeutic agents that interfere with the binding of the HIV envelope glycoprotein gp120 to the CD4 receptor (e.g., PRO 542, PRO 2000, and CV-N) or the coreceptors CCR5 and CXCR4 (e.g., SCH-C and AMD3100) are briefly outlined in this review. The anti-HIV activity of cyclotriazadisulfonamides, a novel class of compounds with a unique mode of action by down-modulating the CD4 receptor in lymphocytic and monocytic cells, is especially highlighted. On the basis of the successful results of T-20, the first approved entry inhibitor, the development of effective antiretrovirals that block HIV entry will certainly be further encouraged.
Full-vectorial finite element method in a cylindrical coordinate system for loss analysis of photonic wire bends (2006)

This paper presents a new full-vectorial finite-element method in a local cylindrical coordinate system, to effectively analyze bending losses in photonic wires. The discretization is performed in the cross section of a three-dimensional curved waveguide, using hybrid edge/nodal elements. The solution region is truncated by anisotropic, perfectly matched layers in the cylindrical coordinate system, to deal properly with leaky modes of the waveguide. This approach is used to evaluate bending losses in silicon wire waveguides. The numerical results of the present approach are compared with results calculated with an equivalent straight waveguide approach and with reported experimental data. These comparisons together demonstrate the validity of the present approach based on the cylindrical coordinate system and also clarifies the limited validity of the equivalent straight waveguide approximation.
Rate-Splitting Multiple Access for Downlink Multi-Antenna Communications: Physical Layer Design and Link-level Simulations (2020)

Rate-Splitting Multiple Access (RSMA) is an emerging flexible, robust and powerful multiple access scheme for downlink multi-antenna wireless networks. RSMA relies on multi-antenna Rate-Splitting (RS) strategies at the transmitter and Successive Interference Cancellation (SIC) at the receivers, and has the unique ability to partially decode interference and partially treat interference as noise so as to softly bridge the two extremes of fully decoding interference (as in Non-Orthogonal Multiple Access, NOMA) and treating interference as noise (as in Space Division Multiple Access, SDMA or Multi-User Multiple-Input Multiple-Output, MU-MIMO). RSMA has been shown to provide significant room for spectral efficiency, energy efficiency, Quality-of-Service enhancements, robustness to Channel State Information (CSI) imperfections, as well as feedback overhead and complexity reduction, in a wide range of network loads (underloaded and overloaded regimes) and user deployments (with a diversity of channel directions, channel strengths and qualities). RSMA is also deeply rooted and motivated by recent advances in understanding the fundamental limits of multi-antenna networks with imperfect CSI at the Transmitter (CSIT). In this work, we leverage recent results on the optimization of RSMA and design for the first time its physical layer, accounting for modulation, coding (using polar codes), message split, adaptive modulation and coding, and SIC receiver. Link-level evaluations confirm the significant throughput benefits of RSMA over various baselines as SDMA and NOMA.
Error recovery service for IEEE 802.11b protocols via adaptive forward error correction and dynamic packet sizing (2004)

We develop a service that allows the current IEEE 802.11b MAC protocol to perform dynamic packet sizing and forward error correction. Our service, called ERSMAC, is designed to allow the deployment of the IEEE 802.11b protocol in industrial environments characterized by high BER and fast time variation. ERSMAC uses a maximum likelihood estimate of the BER to solve for the optimal packet size that maximizes the success probability of transmissions while minimizing the overhead cost. ERSMAC also implements an adaptive forward error correction scheme using Reed-Solomon codes such that every retransmission attempt has a higher probability of success than the previous attempt due to its association with a stronger RS code. Finally, we show, through simulations, that ERSMAC outperforms the original unmodified IEEE 802.116 protocol in terms of average throughput, average delay and efficiency.
Myocardial hypertrophy in the absence of external stimuli is induced by angiogenesis in mice (2007)

Although studies have suggested a role for angiogenesis in determining heart size during conditions demanding enhanced cardiac performance, the role of EC mass in determining the normal organ size is poorly understood. To explore the relationship between cardiac vasculature and normal heart size, we generated a transgenic mouse with a regulatable expression of the secreted angiogenic growth factor PR39 in cardiomyocytes. A significant change in adult mouse EC mass was apparent by 3 weeks following PR39 induction. Heart weight; cardiomyocyte size; vascular density normalization; upregulation of hypertrophy markers including atrial natriuretic factor, beta-MHC, and GATA4; and activation of the Akt and MAP kinase pathways were observed at 6 weeks post-induction. Treatment of PR39-induced mice with the eNOS inhibitor L-NAME in the last 3 weeks of a 6-week stimulation period resulted in a significant suppression of heart growth and a reduction in hypertrophic marker expression. Injection of PR39 or another angiogenic growth factor, VEGF-B, into murine hearts during myocardial infarction led to induction of myocardial hypertrophy and restoration of myocardial function. Thus stimulation of vascular growth in normal adult mouse hearts leads to an increase in cardiac mass.
Cross-platform (NXE-NXT) machine-to-machine overlay matching supporting next node chip manufacturing (2018)

EUV lithography enables the transition from multiple patterning in DUV back to single patterning in EUV, with the associated cost benefit. While imaging and patterning becomes easier with EUV, cross-platform overlay performance needs to be taken into account. With quadruple patterning, the matching performance is driven by the platform capabilities, with platform specific fingerprints not contributing to the matching performance as they are similar for each layer. Introducing EUV automatically means we need to compensate for the differences in the platform fingerprints, as they bring a penalty in the DUV-EUV matching budget. This paper will explain what the main overlay contributors in cross-platform matched machine overlay are and how they can be cancelled or reduced using additional correction measures, with the goal to reach below 2.0 nm cross matched machine overlay.
Proposed Role of Embedded Dentin Chips for the Clinical Failure of Nickel-Titanium Rotary Instruments (2004)

Discarded ProFile and ProTaper nickel-titanium rotary instruments, with unknown history of clinical use, were obtained from graduate endodontic clinics at Ohio State University and University of Texas Health Science Center at Houston Dental Branch. These discarded instruments and as-received instruments of both types were examined with a scanning electron microscope to investigate effects of clinical use and causes of failure. For used ProTaper instruments, dentinal debris was wedged mostly in narrow, radial, land-type regions and less on convex flute surfaces. For used ProFile instruments, dentinal debris was wedged mostly in the metal rollover and on concave flute surfaces. Used instruments of both types exhibited widened machining grooves, and elongated and stretched roll-over. Dentin chips were wedged in surface micro-cracks that appeared to propagate from original machining flaws and widen during in vivo root canal preparation. From our observational study, wedged dentinal deposits seem to play a pivotal role for clinical failure of these instruments.
Gas Channels for NH 3 : Proteins from Hyperthermophiles Complement an Escherichia coli Mutant (2002)

Ammonium transport (Amt) proteins appear to be bidirectional channels for NH(3). The amt genes of the hyperthermophiles Aquifex aeolicus and Methanococcus jannaschii complement enteric amtB mutants for growth at 25 nM NH(3) at 37 degrees C. To our knowledge, Amt proteins are the first hyperthermophilic membrane transport proteins shown to be active in a mesophilic bacterium. Despite low expression levels, His-tagged Aquifex Amt could be purified by heating and nickel chelate affinity chromatography. It could be studied genetically in Escherichia coli.