gebhart/patrepeval huggingface dataset:
Out-of-order issue logic using sorting networks (2010)

A fundamental property of superscalar architectures is the execution of multiple instructions per cycle. To accomplish this, the issue logic selects and prioritizes the instructions whose operands will be ready in the next cycle, using wakeup, select and queue update logic. By incorporating the issue logic in one pipeline stage, dependent instructions can be issued in consecutive cycles. However, the many serial operations required makes this problematic from a circuit delay perspective. In this paper, we propose an issue queue design that divides the ready signals into groups, sorts the groups in parallel and provides four oldest ready instructions for issue, with single-cycle operation. Static CMOS select and update logic reduces power and low fan-out in many stages improves circuit speed. The complete issue logic requires 30 inversions, allowing simulated circuit operation at over 3 GHz in a foundry 45nm SOI fabrication process.
[Cavernous angioma of the cervical spinal cord]. (1992)

A 34-year old man gradually developed a paraparesis which spontaneously regressed within a few months. One year later, the patient suffered from acute torticollis immediately followed by flaccid tetraparesis with pyramidal signs, dissociated sensory deficit and acute retention of urine. Magnetic resonance imaging (MRI) showed, in the cervical cord, a vascular malformation that was not opacified at angiography. The lesion, a cavernous angioma, was surgically removed, leading to recovery. So far, thirty five cases of spinal cord angioma have been published, most of them since the advent of MRI which makes it possible to determine the exact incidence of this lesion, as well as its signs, symptoms and course.
α-Synuclein phosphorylation at serine 129 occurs after initial protein deposition and inhibits seeded fibril formation and toxicity (2022)

α-Synuclein (α-syn) phosphorylation at serine 129 (pS129–α-syn) is substantially increased in Lewy body disease, such as Parkinson’s disease (PD) and dementia with Lewy bodies (DLB). However, the pathogenic relevance of pS129–α-syn remains controversial, so we sought to identify when pS129 modification occurs during α-syn aggregation and its role in initiation, progression and cellular toxicity of disease. Using diverse aggregation assays, including real-time quaking-induced conversion (RT-QuIC) on brain homogenates from PD and DLB cases, we demonstrated that pS129–α-syn inhibits α-syn fibril formation and seeded aggregation. We also identified lower seeding propensity of pS129–α-syn in cultured cells and correspondingly attenuated cellular toxicity. To build upon these findings, we developed a monoclonal antibody (4B1) specifically recognizing nonphosphorylated S129–α-syn (WT–α-syn) and noted that S129 residue is more efficiently phosphorylated when the protein is aggregated. Using this antibody, we characterized the time-course of α-syn phosphorylation in organotypic mouse hippocampal cultures and mice injected with α-syn preformed fibrils, and we observed aggregation of nonphosphorylated α-syn followed by later pS129–α-syn. Furthermore, in postmortem brain tissue from PD and DLB patients, we observed an inverse relationship between relative abundance of nonphosphorylated α-syn and disease duration. These findings suggest that pS129–α-syn occurs subsequent to initial protein aggregation and apparently inhibits further aggregation. This could possibly imply a potential protective role for pS129–α-syn, which has major implications for understanding the pathobiology of Lewy body disease and the continued use of reduced pS129–α-syn as a measure of efficacy in clinical trials.
Performance of content replication in MobiTribe: A distributed architecture for mobile UGC sharing (2011)

An increasing portion of traffic in mobile networks conies from users creating content and uploading it to the Internet to share it. The capacity of mobile networks is a limited resource and uploading high resolution content consumes a large part of it. We introduce MobiTribe, a distributed storage cloud consisting of mobile devices for storing the content created on the phones. It can serve requests for content and take advantage of networks with spare capacity to deliver the content at a lower cost. We propose a content distribution and replication algorithm which achieves this goal. The performance of the algorithm is evaluated using empirical data traces of WLAN availability patterns of mobile devices, showing that it is possible to achieve 99.98% availability of a content via WLAN while minimising content distribution to an average of 2.69 replicas.
New organogelators based on cyclotriveratrylene platforms bearing 2-dimethylacetal-5-carbonylpyridine fragments (2007)

Gelators, compounds able to solidify solvents, and in particular hydrogelators are interesting soft materials. In this paper we have synthesized cyclotriveratrylene (CTV) platforms symmetrically end-substituted with pendent primary amines or nicotamic substituents. These non-amphiphilic structures induce self-assembly in a large variety of solvents forming robust and opaque gels. Cyclotriveratrylene gels have for the first time been formed and characterized using FT-IR and freeze fracture electron microscopy. Two hierarchical events are responsible for the gel structure. Individual fibres of 4–5 nm diameter are formed by aggregation of the functionalised CTV molecules. These fibres then further self-assemble into large ribbons several µm long and 20 to 40 nm wide. Within the ribbons the fine striations observed by FFEM are due to individual straight chains organized in a highly compacted state. Within the fibres the individual CTV molecules are held together by hydrogen bonding of the amide function as probed by infra-red spectroscopy.
Preparative Thioacidolysis of Spruce Lignin: Isolation and Identification of Main Monomeric Products (1986)

Structure des diastereoisomeres de type thioethylphenylpropane issus des thioacidolyses de lignine par chromatographie preparative combinee a la RMN et la spectroscopie de masse haute resolution
Kynurenic acid derivatives. Structure-activity relationships for excitatory amino acid antagonism and identification of potent and selective antagonists at the glycine site on the N-methyl-D-aspartate receptor (1991)

Derivatives of the nonselective excitatory amino acid antagonist kynurenic acid (4-oxo-1,4-dihydroquinoline-2-carboxylic acid, 1) have been synthesized and evaluated for in vitro antagonist activity at the excitatory amino acid receptors sensitive to N-methyl-D-aspartic acid (NMDA), quisqualic acid (QUIS or AMPA), and kainic acid (KA). Introduction of substituents at the 5-, 7-, and 5,7-positions resulted in analogues having selective NMDA antagonist action, as a result of blockade of the glycine modulatory (or coagonist) site on the NMDA receptor. Regression analysis suggested a requirement for optimally sized, hydrophobic 5- and 7-substituents, with bulk tolerance being greater at the 5-position. Optimization led to the 5-iodo-7-chloro derivative (53), which is the most potent and selective glycine/NMDA antagonist to date (IC50 vs [3H]glycine binding, 32 nM; IC50's for other excitatory amino acid receptor sites, greater than 100 microM). Substitution of 1 at the 6-position resulted in compounds having selective non-NMDA antagonism and 8-substituted compounds were inactive at all receptors. The retention of glycine/NMDA antagonist activity in heterocyclic ring modified analogues, such as the oxanilide 69 and the 2-carboxybenzimidazole 70, suggests that the 4-oxo tautomer of 1 and its derivatives is required for activity. Structurally related quinoxaline-2,3-diones are also glycine/NMDA antagonists, but are not selective and are less potent than the 1 derivatives, and additionally show different structure-activity requirements for aromatic ring substitution. On the basis of these results, a model accounting for glycine receptor binding of the 1 derived antagonists is proposed, comprising (a) size-limited, hydrophobic binding of the benzene ring, (b) hydrogen-bond acceptance by the 4-oxo group, (c) hydrogen-bond donation by the 1-amino group, and (d) a Coulombic attraction of the 2-carboxylate. The model can also account for the binding of quinoxaline-2,3-diones, quinoxalic acids, and 2-carboxybenzimidazoles.
A 2-gigawatt, 1-microsecond, microwave source (1996)

For the last decade or more, researchers in a number of US government laboratories have been attempting to develop L-band microwave sources capable of generating one or more gigawatts, with one-microsecond pulses. In order to produce the required high beam currents, the common approach has been to employ field emission cathodes. For this and other reasons the devices which have been built (MILOs, RKAs, relativistic magnetrons) have operated with a poor vacuum, a condition not consistent with the necessity to hold off the very high rf and dc gradients encountered at these power levels. As a result, the microsecond goal has never been attained. Although in some cases several gigawatts have been generated, pulse duration is limited to about 100 ns. This condition is referred to as “pulse shortening”. The proposed source is based on periodic magnetic (PPM) focusing and is an outgrowth of work performed at SLAC on very high peak power X-band klystrons for a future electron-positron linear collider. These tubes must be focused with permanent magnets, for economic reasons. The new device (GMBK, for Gigawatt Multiple Beam Klystron) is entirely within the state-of-the-art and need only depend on good vacuum tube practice to perform to its specification. It employs thermionic cathodes, loaded to about 40 A/cm
 2
, a current density which is within the state-of-the-art for microsecond pulses.
Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design (2017)

Among broadly neutralizing antibodies to HIV, 10E8 exhibits greater neutralizing breadth than most. Consequently, this antibody is the focus of prophylactic/therapeutic development. The 10E8 epitope has been identified as the conserved membrane proximal external region (MPER) of gp41 subunit of the envelope (Env) viral glycoprotein and is a major vaccine target. However, the MPER is proximal to the viral membrane and may be laterally inserted into the membrane in the Env prefusion form. Nevertheless, 10E8 has not been reported to have significant lipid-binding reactivity. Here we report x-ray structures of lipid complexes with 10E8 and a scaffolded MPER construct and mutagenesis studies that provide evidence that the 10E8 epitope is composed of both MPER and lipid. 10E8 engages lipids through a specific lipid head group interaction site and a basic and polar surface on the light chain. In the model that we constructed, the MPER would then be essentially perpendicular to the virion membrane during 10E8 neutralization of HIV-1. As the viral membrane likely also plays a role in selecting for the germline antibody as well as size and residue composition of MPER antibody complementarity determining regions, the identification of lipid interaction sites and the MPER orientation with regard to the viral membrane surface during 10E8 engagement can be of great utility for immunogen and therapeutic design.
Intragenic breakpoint within RAD51L1 in a t(6;14)(p21.3;q24) of a pulmonary chondroid hamartoma (2001)

Rearrangements involving chromosome region 14q23-->q24 represent a main cytogenetic subgroup in a variety of benign solid tumors. Recently, in uterine leiomyomas containing the classical t(12;14)(q15;q23-->q24), the primary chromosome 14 target gene was identified as the protein kinase-encoding gene RAD51L1. In this report we show that RAD51L1 is also involved in the frequently occurring t(6;14) (p21;q23-->q24) in pulmonary chondroid hamartomas.
Figure S5 from TGFβ Blockade Augments PD-1 Inhibition to Promote T-Cell–Mediated Regression of Pancreatic Cancer (2023)

&lt;p&gt;Figure S5 shows additional H&amp;E stained sections from Galunisertib and/or anti-PD-1 treated mice.&lt;/p&gt;
ChemInform Abstract: SIX‐MEMBERED RING PHOSPHITES IN TWIST CONFORMATIONS. THE METHYL AND PHENYL TRANS‐3′,5′‐CYCLIC PHOSPHITES OF THYMIDINE (1984)

Abstract Die Addition von Methanol oder Phenol an das P‐Amid (I) in Gegenwart von Pyridiniumchlorid liefen die Phosphite (II) als cis/trans‐I)iastereomerengemische mit 80proz. Anteil der thermodynamisch instabileren trans‐Diastereomeren (trans‐Stellung von Tzum OR‐Substituenten).
Ionosphere Scintillation Signal Parameters Modeling Based on Triple Frequency Software GNSS Receiver Measurements (2012)

Ionosphere scintillations can cause significant amplitude and/or phase fluctuations of GNSS signals. This paper presents studies of scintillation effects on the new GPS L2C, and L5 signals based on data collected using a GNSS receiver array at the HAARP facility in Alaska. The receivers used in this study includes a custom narrow-band front end that collects GPS L1 and L2 IF samples and a reconfigurable USRP2-based RF front end to collect wideband GPS L5 signals. Ionosphere scintillation are expected to have stronger impacts on the new GPS L2C and L5 signals due to their lower carrier frequencies compared to L1. This paper presents quantitative relationships among GPS L1, L2, and L5 carrier tracking results based on eight natural scintillation events during 2011. The results confirm that scintillation has a stronger impact on GPS L2 and L5 signals than on the L1 signal and that carrier phase and amplitude scintillations on different frequency channels are highly correlated.
Applied mechanics for humans: challenges in sports engineering (2006)

This paper describes some of the challenges encountered when applying mechanical principles to human biomechanical problems, using examples from the author’s experience in sports-related research and product development. As a mechanical system, the human body is unlike any man-made machine or mechanism. Its framework adapts to support habitual loads. Its actuators rely heavily on elastic properties and appear to regulate the stiffness of limbs rather the applied force or displacement. Its motion control systems can appear chaotic, with the consequence that even repetitive, cyclic movements patterns (e.g. walking and running) are highly variable. A speed suit development project illustrates the contribution a biomechanical perspective can bring to a sports engineering project. In this case, kinematic analyses of sprinters and speed skaters were used to document the continually varying velocities and orientations of the body’s segments relative to the air flow. This information allowed the aerodynamicists to test suit materials under appropriate conditions and to select different materials for different parts of the suit. As a second example, the selection of materials for American Football helmets begins as a classical cushioning design problem. Empirical descriptions of the impact tolerance of the head constrain the possible solution but helmets can be engineered to prevent skull fractures and traumatic brain injuries. The prevention of mild traumatic brain injury (concussion) remains an unsolved problem, however, and a mechanical solution may not exist. In comparison to a helmet, athletic shoe cushioning systems are required to handle relatively low forces and impact energies. Designing a running shoe that attenuates impact shock is, mechanically speaking, a relatively trivial task. The mechanical processes underlying some other important, related functions of the sports shoe are less well defined. “Comfort” and other perceptual responses, for example, are harder to measure than impact shock, and consequently more difficult to engineer. The application of mechanical principles to human biomechanical problems can generate some unique problems, but the paths taken in an effort to find innovative, practical solutions will be familiar to engineers working almost any field.
ADAPTIVE DIAGNOSTIC SYSTEM PROJECT (1998)

This Innovations Deserving Exploratory Analysis (IDEA) project sought to integrate state-of-the-art, off-the-shelf hardware and software components with custom-designed software and hardware interfaces to provide a cost-effective general testing platform for use at the San Francisco Bay Area Rapid Transit District (BART). This Adaptive Diagnostic System (ADS) was to be developed initially to service two particular Units Under Test (UUTs) in the BART Electronic Repair Shop. The project was successful in achieving its main technical objectives. The ADS general framework provided most of the basic features desired. It employed excellent graphical user interfaces, and was capable of providing a rapid and precise automated test of one of the two UUTs. The architecture of the software was developed in such a way that it could be adapted easily to test other UUTs and to incorporate other test instruments. The neural network diagnostic module was developed and refined to the point that it could recognize with high probability waveforms that were discernable by the human eye. Using a single generalized architecture, the module produced neural networks that were trainable to recognize two rather different classes of waveforms associated with the two UUTs: modulated carrier, and transient response to a step function input. Principal development effort was associated with the design of the feature reduction preprocessing functions, and the training and testing software.
Genotype-independent plant transformation (2022)

Plant transformation and regeneration remain highly species- and genotype-dependent. Conventional hormone-based plant regeneration via somatic embryogenesis or organogenesis is tedious, time-consuming, and requires specialized skills and experience. Over the last 40 years, significant advances have been made to elucidate the molecular mechanisms underlying embryogenesis and organogenesis. These pioneering studies have led to a better understanding of the key steps and factors involved in plant regeneration, resulting in the identification of crucial growth and developmental regulatory genes that can dramatically improve regeneration efficiency, shorten transformation time, and make transformation of recalcitrant genotypes possible. Co-opting these regulatory genes offers great potential to develop innovative genotype-independent genetic transformation methods for various plant species, including specialty crops. Further developing these approaches has the potential to result in plant transformation without the use of hormones, antibiotics, selectable marker genes, or tissue culture. As an enabling technology, the use of these regulatory genes has great potential to enable the application of advanced breeding technologies such as genetic engineering and gene editing for crop improvement in transformation-recalcitrant crops and cultivars. This review will discuss the recent advances in the use of regulatory genes in plant transformation and regeneration, and their potential to facilitate genotype-independent plant transformation and regeneration.
Optimization based automated curation of metabolic reconstructions (2007)

We have proposed systematic methods to identify and fill gaps in genome-scale metabolic reconstructions. The identified gaps can be filled both by making modifications in the existing model and by adding missing reactions by reconciling multi-organism databases of reactions with existing genome-scale models. Computational results provide a list of hypotheses to be queried further and tested experimentally.
Enhanced Expression of Chicken Cystatin as a Thioredoxin Fusion Form in Escherichia coli AD494(DE3)pLysS and Its Effect on the Prevention of Surimi Gel Softening (2002)

The DNA encoding chicken lung cystatin was ligated into a thioredoxin-pET 23a+ expression vector and transformed into Escherichia coli AD494(DE3)pLysS. A high level of soluble recombinant thioredoxin-cystatin (trx-cystatin) was expressed in the cytoplasm of the E. coli transformant. As compared with recombinant cystatin (trx-free), a 38.7% increase of inhibitory activity in the soluble fraction was achieved by introducing the trx fusion protein. Trx-cystatin was purified to electrophoretical homogeneity by 3 min of heating at 90 degrees C and Sephacryl S-100 chromatography. The molecular mass of trx-cystatin was 29 kDa, which was the expected size based on its composition of recombinant trx (16 kDa) and chicken cystatin (13 kDa). The purified trx-cystatin behaved as a thermally stable and papain-like proteinase inhibitor comparable to either recombinant or natural chicken cystatins. The inhibitor could inhibit the gel softening of mackerel surimi.
Supplementary Figure 5 from Mobilization of CD8<sup>+</sup> T Cells via CXCR4 Blockade Facilitates PD-1 Checkpoint Therapy in Human Pancreatic Cancer (2023)

&lt;p&gt;Live microscopy analysis of CD8+ T cell distribution in slice cultures&lt;/p&gt;
A strategic framework for novel drug development in multiple myeloma (2007)

Summary Although multiple myeloma remains incurable, recent advances in research have created a new paradigm for the development of novel agents for myeloma treatment. Biological insights are being translated rapidly from bench to bedside, with an increasing number of agents available at all stages of disease. Concomitantly, the drug development and approval process has become more challenging. Defining optimal clinical dosing schedules and therapeutic regimens is increasingly dependent on insights derived from genomic, proteomic and cell signaling studies. Because the maximum tolerated dose of a novel agent may not be the same as the optimal biological dose, designing phase I trials is more complex. Evaluation of new agents in patients who have relapsed is more challenging because the number of effective therapies has increased. Finally, choosing a ‘standard therapy’ control arm for randomised trials is more difficult because of the increased number of potential comparator regimens. In June 2005, the Multiple Myeloma Research Foundation (MMRF) sponsored a roundtable symposium in Washington, DC, to define the strategies and guidelines for phases I, II and III development of new myeloma agents, with the ultimate goal of speeding delivery of new therapies to myeloma patients.
Antioxidant Treatment Prevents Renal Damage and Dysfunction and Reduces Arterial Pressure in Salt-Sensitive Hypertension (2005)

The goal of this study was to test the hypothesis that oxidative stress in Dahl salt-sensitive (SS) rats on a high-sodium intake contributes to the progression of renal damage, the decreases in renal hemodynamics, and the development of hypertension. We specifically studied whether antioxidant therapy, using vitamins C and E, could help prevent renal damage and glomerular filtration rate (GFR) and renal plasma flow reductions and attenuate the increases in arterial pressure. Thirty-three 7- to 8-week old Dahl SS/Rapp strain rats were placed on either a high-sodium (8%) or a low-sodium (0.3%) diet with or without vitamin E (111 IU/d) in the food and 98 mg/d vitamin C in the drinking water for 5 weeks. Rats were equipped with indwelling arterial and venous catheters at day 21. By day 35 in the rats with high-sodium diet, vitamin C and E treatment significantly decreased renal cortical and medullary O2*- release, mean arterial pressure, urinary protein excretion, glomerular necrosis, and renal tubulointerstitial damage. At this time, GFR significantly decreased in the high-sodium diet group (1.6+/-0.2 mL/min) when compared with either the high-sodium plus vitamins C and E (2.9+/-0.2 mL/min) or the low-sodium diet group (2.9+/-0.3 mL/min). In SS rats on high-sodium diet, renal plasma flow decreased 40%, and this reduced flow was restored by vitamin treatment. In Dahl salt-sensitive hypertension, increased oxidative stress plays an important role in the renal damage, decreases in renal hemodynamics, and increases in arterial pressure that occur. Antioxidant treatment with vitamins C and E improves renal dysfunction, lessens renal injury, and decreases arterial pressure in Dahl salt-sensitive hypertension.