gebhart/patrepeval huggingface dataset:
Matrix-matrix multiplication on a large register file architecture with indirection (2014)

Dense matrix-matrix multiply is an important kernel in many high performance computing applications including the emerging deep neural network based cognitive computing applications. Graphical processing units (GPU) have been very successful in handling dense matrix-matrix multiply in a variety of applications. However, recent research has shown that GPUs are very inefficient in using the available compute resources on the silicon for matrix multiply in terms of utilization of peak floating point operations per second (FLOPS). In this paper, we show that an architecture with a large register file supported by “indirection ” can utilize the floating point computing resources on the processor much more efficiently. A key feature of our proposed in-line accelerator is a bank-based very-large register file, with embedded SIMD support. This processor-in-regfile (PIR) strategy is implemented as local computation elements (LCEs) attached to each bank, overcoming the limited number of register file ports. Because each LCE is a SIMD computation element, and all of them can proceed concurrently, the PIR approach constitutes a highly-parallel super-wide-SIMD device. We show that we can achieve more than 25% better performance than the best known results for matrix multiply using GPUs. This is achieved using far lesser floating point computing units and hence lesser silicon area and power. We also show that architecture blends well with the Strassen and Winograd matrix multiply algorithms. We optimize the selective data parallelism that the LCEs enable for these algorithms and study the area-performance trade-offs.
Endoscopic drainage of the main pancreatic duct for chronic pancreatitis: Indications, techniques and long-term results (1997)

SCOPUS: cp.j
Enhanced emergency communication using mobile sensing and MANET (2012)

Emergency response services are often delayed due to the destruction or non-availability of the communication network. This research work proposes Mobile Adhoc NETwork (MANET) architecture integrated with mobile sensing concepts, for reviving the communication network in disaster hit areas. Mobile sensing in emergency scenarios can very well address issues like victim localization etc. and offer help in providing specific information about the affected area to the responders and control stations. This paper proposes a design that utilizes the existing the mobile devices such as smartphones, laptops, etc. in the field to provide the required communication facility. A new buffer system powered flooding methodology is also proposed to cater to the challenging environment. The mobile adhoc network architecture proposed is implemented and tested using several android based mobile phones. An android application named Android app for Emergency Communication (AEC) was developed and it enabled users to send messages to emergency services as well as their dear ones even when they are in regions with no cellular coverage.
Evaluation of applying IHC4 as a prognostic model in the translational study of Intergroup Exemestane Study (IES): PathIES (2017)

In the PathIES population, the IHC4 score is useful in predicting long-term relapse in patients who remain disease-free after 2-3 years. This is a first trial to suggest the extending use of IHC4+C score for prognostic indication for patients who have switched endocrine therapies at 2-3 years and who remain disease-free after 2-3 years.
Lipase-catalysed Baeyer–Villiger reactions (1995)

S. C. Lemoult, P. F. Richardson and S. M. Roberts, J. Chem. Soc., Perkin Trans. 1, 1995, 89 DOI: 10.1039/P19950000089
The Effect of Unconventional Piston Movement on SI Engine Combustion and Emissions (2005)

&lt;div class="htmlview paragraph"&gt;A major trend in current automotive research is hybridization of the power supply. This combination of electrical machine and combustion engine results, in some hybridization topologies, in a total decoupling of the combustion engine from the transmission. When the engine is decoupled from the transmission a new degree of freedom arises in engine design. The piston movement does not have to follow an evenly rotating shaft any more. It can be altered by the generator to achieve a movement found to be better from the point of efficiency or environmental concerns.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Modelling work showed a potential of lowered NO emissions if the expansion could be delayed. The experimental study, conducted in a two piston Alvar engine, showed that the state of the art electrical machine (EM) propelling one of the crankshafts was too weak to change the crankshaft speed in an extent to give the fast volume changes required to change the emissions of the internal combustion engine (ICE). By running the EM at four times the speed of the dynamometer coupled to the other piston, more unorthodox volume traces were generated and differences in the emissions of the engine were found. None of the possible changed volume traces generated pressure traces showing major changes in the 10-90% heat release rate of the engine. The experiments were conducted at the limit of what the EM was able to achieve at all times.&lt;/div&gt;
An effective processor allocation strategy for multiprogrammed shared-memory multiprocessors (1997)

Existing techniques for sharing the processing resources in multiprogrammed shared-memory multiprocessors, such as time-sharing, space-sharing, and gang-scheduling, typically sacrifice the performance of individual parallel applications to improve overall system utilization. We present a new processor allocation technique called Loop-Level Process Control (LLPC) that dynamically adjusts the number of processors an application is allowed to use for the execution of each parallel section of code, based on the current system load. This approach exploits the maximum parallelism possible for each application without overloading the system. We implement our scheme on a Silicon Graphics Challenge multiprocessor system and evaluate its performance using applications from the Perfect Club benchmark suite and synthetic benchmarks. Our approach shows significant improvements over traditional time-sharing and gang-scheduling. It has performance comparable to, or slightly better than, static space-sharing, but our strategy is more robust since, unlike static space-sharing, it does not require a priori knowledge of the applications' parallelism characteristics.
Tapered fiber bundles for combining laser pumps (Invited Paper) (2005)

A tapered fiber bundle is one of the leading approaches to coupling pump light into cladding-pumped fibers. This article compares it to other pump coupling schemes, and describes the tapered fiber bundle in detail. In addition tapered fiber bundles which maintain the polarization state of the signal and transform the size of the mode are described.
Optical Multi-Band Networks: Maximizing Lifetime of Deployed Fiber Infrastructure (2019)

Optical multi-band networks provide an option for scaling the capacity of single-mode fiber with the continuously increasing demand. Achievable capacities are reviewed and challenges to realize them in deployed systems are highlighted.
Time Reversal of Ultrasound through a Phononic Crystal (2006)

In this Letter, we experimentally investigate time reversal focusing through a phononic crystal consisting of a periodic square arrangement of steel rods in water. An acoustic pulse is transmitted through the medium, received at a transducer array, time reversed and backpropagated. Both spatial focusing and time compression are studied and compared with those obtained through an equivalent disordered medium. With the phononic crystal, we do not observe the "hyperfocusing effect" that is typical of time reversal through disordered samples.
One‐Pot Synthesis of Furo‐ or Thienoquinolines through Sequential Imination and Intramolecular Palladium‐Catalyzed Direct Arylation (2012)

Abstract The sequential imination and intramolecular palladium‐catalyzed direct arylation of thiophene‐3‐carbaldehyde or furan‐3‐carbaldehyde with 2‐haloanilines provided a one‐pot access to furo‐ or thienoquinolines in high yields with H 2 O and HBr as the major waste. Both electron‐withdrawing and ‐donating substituents on the 2‐haloaniline derivatives were tolerated. These furo‐ or thienoquinoline derivatives can be employed in the direct arylation at C‐5 of the furyl or thienyl moiety, and a variety of corresponding arylation products were obtained in high yields.
A Study on Fundamental Properties of PSP in Low Pressure Region. (2002)

Recently pressure sensitive paint (PSP) has actively developed to measure continuous distribution of the surface pressure. However, the pressure range has been limited above 1 Torr (133.3 Pa) and there is no application to lower pressure range because the pressure sensitivity seems to be not so high in that range. In this study, we apply three types of PSP [two types are composed by organic dye and polymer (luminophore/binder) ; PtOEP/GP 197 and PtTFPP/poly (TMSP), and another one is Bath-Ru adsorbed on anodized aluminum] to the rarefied gas flow mainly lower than 1 Torr and examine those fundamental properties, such as pressure/temperature sensitivity and time response of luminescence and so on, leading to selection of the most suitable PSP among them for the low pressure range. Finally, the pressure distribution of the surface on which a low density supersonic free jet impinges is measured by the PSP.
MACVIA-ARIA Sentinel NetworK for allergic rhinitis (MASK-rhinitis) (2015)

Several unmet needs have been identified in allergic rhinitis: identification of the time of onset of the pollen season, optimal control of rhinitis and comorbidities, patient stratification, multidisciplinary team for integrated care pathways, innovation in clinical trials and, above all, patient empowerment. MASK-rhinitis (MACVIA-ARIA Sentinel NetworK for allergic rhinitis) is a simple system centred around the patient which was devised to fill many of these gaps using Information and Communications Technology (ICT) tools and a clinical decision support system (CDSS) based on the most widely used guideline in allergic rhinitis and its asthma comorbidity (ARIA 2015 revision). It is one of the implementation systems of Action Plan B3 of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA). Three tools are used for the electronic monitoring of allergic diseases: a cell phone-based daily visual analogue scale (VAS) assessment of disease control, CARAT (Control of Allergic Rhinitis and Asthma Test) and e-Allergy screening (premedical system of early diagnosis of allergy and asthma based on online tools). These tools are combined with a clinical decision support system (CDSS) and are available in many languages. An e-CRF and an e-learning tool complete MASK. MASK is flexible and other tools can be added. It appears to be an advanced, global and integrated ICT answer for many unmet needs in allergic diseases which will improve policies and standards.
Relation of cell surface antigens on methylcholanthrene-induced fibrosarcomas to immunoglobulin heavy chain complex variable region-linked T cell interaction molecules (1983)

For optimal activation, T suppressor cells must receive a signal froma specialized inducer cell. The activating signal is delivered by a molecular complex that is composed, in part, of polymorphic gene products that are controlled by the immunoglobulin heavy chain complex (Igh) and that map to the variable region (Igh-V) of the complex. Consequently, if suppressor/inducer cells and their acceptor cells do not share Igh-V-encoded polymorphisms, the inducer molecules fail to activate the suppressor cells. Other polymorphic gene products (those that act as transplantation antigens on methylcholanthrene-induced fibrosarcomas) have been shown to be encoded by a gene(s) that maps to the same general region of chromosome 12 as does the Igh complex. Therefore, we tested the hypothesis that polymorphic gene products expressed by the T suppressor/inducer cell and its biologically active product were related to the transplantation antigens on these fibrosarcomas. We have found that isoantisera directed to a number of BALB/c methylcholanthrene-induced tumors block the induction of T suppressor cells but they do so only if the inducer or acceptor T cell (or both) expresses BALB/c Igh-linked polymorphisms. All other BALB/c gene products are irrelevant. These findings suggest that "transformation related antigens" on some sarcoma cells are variants of, or are otherwise related to, the cell interaction molecules that T cell subsets use to communicate with one another under normal circumstances. Furthermore, the findings that (a) multiple methylcholanthrene-induced tumors express serologically related antigens (as well as the unique ones that have been previously demonstrated by transplantation tests) and (b) these serologically related antigens can be found on Igh-V-controlled T cell communication molecules raise the intriguing possibility that, like certain viruses, methylcholanthrene reacts with specific regions of cellular DNA that either directly or indirectly regulate the expression of other specific genes (in this particular case the genes that encode the T cell communication molecules).
FOXP3 activation in Treg cells, - atomic level aspects of FOXP3 structure and biochemistry that govern function (89.4) (2009)

Abstract The path by which signaling transduction from the cell surface to the nucleus leads to FOXP3 activation and function is undefined. The additional complexity of creation of an ordered FOXP3 ensemble of transcriptional cofactors on chromatin is not understood. FOXP3 activation in Treg cells may be regulated by extra-cellular stimuli that occur through innate, toll-like and cytokine receptors. Our studies found that TCR receptor and pro-inflammatory cytokine signals including TGF-beta and IL-6 regulate FOXP3 binding to DNA in human CD4+CD25+ Treg cells. Here we report our recent progress in understanding the role of cell surface receptor signals and pro-inflammatory cytokines in regulating biochemical modifications of the FOXP3 molecule altering its activity in Treg cells. We have now determined the biochemical features of how pro-inflammatory cytokines and pharmaceutical agents affect FOXP3 activity, and consequently how they may affect immune responses in human inflammatory disease. Moreover, we also have deduced the atomic structure of large parts of the FOXP3 molecule including the zinc finger and leucine zipper domains. These regions are important for dimerization and oligomerization of FOXP3 as well as interactions with other molecules. Our structural and biochemical studies establish the atomic and molecular basis for understanding human XLAAD/IPEX autoimmune diseases. Research grants include NIH AI073489-01A1 (M.I.G.) and Nidus Laboratories (B.L., and Z.Z.).
Nanopackaging solution from clean room to UHV Environment: Hydrogen Passivated Si (100) Substrate Fabrication and Use for Atomic Scale Investigations and Self-Assembled Monolayer Grafting (2016)

Specific surfaces allowing Ultra-High Vacuum (UHV) investigations are required for the successful development of atomic nanostructures. Surface contamination, atomic roughness and defects density must be controlled in order to ensure the reliability of advanced UHV experiments. Surface preparation is a key parameter and is usually conducted in-situ in the UHV chamber. However the surface preparation requires a complex protocol. A microelectronic clean room environment enables the particles density control and enables 200 mm wafer scale developments, especially Si(001)-(2x1):H surface reconstruction. However, this passivated surface is reactive and can be easily deteriorated, particularly during transportation. Consequently, a nanopackaging solution is proposed in order to provide a preserving environment for transportation. The nanopackaging process consists in the direct bonding of two passivated silicon surfaces, and is followed by a wafer dicing step into 1cm2 dies. Samples can be stored, shipped and in-situ opened without additional treatment. Furthermore, these samples can provide a reliable surface onto which molecular grafting can be accomplished. The fabrication modules and the associated characterization results will be described as well as atomic nanostructure manipulations and especially the grafting of a self-assembled monolayer using supercritical carbon dioxide as a medium.
Limits on the lifetimes of intramolecular rovibrational relaxation (1985)

Rotationally resolved infrared laser induced fluorescence spectra are presented for dimethyl ether and methyl formate. Q branch spectra are presented for 1,4-dioxane, methyl formate, and dimethyl carbonate. It has been demonstrated earlier that all of these states intramolecularly vibrationally relax. Lower limits on the lifetime of this process are inferred from the present data. For methyl formate and dimethyl ether the J=1 and 2 states have linewidths &amp;lt;0.31 cm−1. This sets a lower limits on the lifetime of 15 ps, although for the limited number of coupled states an exponential decay is not expected. This is also the lower limit for relaxation in the higher J=20 states of 1,4-dioxane and methyl formate, for which exponential decays probably do occur. Dimethyl carbonate relaxes in greater than 10 ps. All measurements were performed in a pulsed supersonic beam with a infrared optical parametric oscillator.
Data-driven multi-objective optimization tactics for catalytic asymmetric reactions (2022)

Optimization of catalyst structure to simultaneously improve multiple reaction objectives (e.g., yield, enantio-, and regioselectivity) remains a formidable challenge. Herein, we describe a machine learning workflow for the multi-objective optimization of catalytic reactions that employ chiral bisphosphine ligands. This was demonstrated through the optimization of two sequential reactions required in the asymmetric synthesis of an active pharmaceutical ingredient. To accomplish this, a density functional theory-derived database of >500 bisphosphine ligands was constructed and a designer chemical space mapping technique was established. The protocol used classification methods to identify active catalysts, followed by linear regression to model reaction selectivity. This led to the prediction and validation of significantly improved ligands for all reaction outputs suggesting a general strategy for the optimization of reactions where performance is controlled by bisphosphine ligands.
Molecular Features and Survival Outcomes of the Intrinsic Subtypes Within HER2-Positive Breast Cancer (2014)

When the intrinsic subtypes are taken into account, cHER2-positivity does not translate into large changes in the expression of downstream signaling pathways, nor does it affect patient survival in the absence of HER2 targeting.
Electronic Structure of the YDTyrosyl Radical in Photosystem II:  A High-Frequency Electron Paramagnetic Resonance Spectroscopic and Density Functional Theoretical Study (1997)

We report the high-frequency (139.5 GHz) electron paramagnetic resonance (EPR) spectrum of the tyrosyl radical of photosystem II. A rhombic powder pattern with principal g values g1 = 2.007 82, g2 = 2.004 50, and g3 = 2.002 32 is observed. The well-defined turning points and the value of the largest principal g value are indicative of ordered hydrogen bonding to the tyrosyl phenyl oxygen. Hyperfine structure is resolved on all three turning points. Proton hyperfine couplings obtained from the simulation of the 139.5 GHz EPR spectrum are in good agreement with X-band electron spin echo−electron nuclear double resonance studies. The high-frequency EPR spectrum was acquired under conditions of saturation in which the dispersion signal is detected. Proper replication of the high-frequency EPR spectral features is only achieved in simulations which account for the line shapes characteristic of saturated dispersion signals. Comparison of the spectrum with spectra of non-hydrogen bonded tyrosyl radicals indicates that the largest principal g value (g1), oriented along the C−O bond, is sensitive to hydrogen bonding at the phenyl oxygen. Density functional calculations indicate that the decreased downfield shift in g1 from the free electron g value with increasing hydrogen bond strength arises from both a decreased spin density on the phenyl oxygen5−30% over a range of reasonable hydrogen bond distances (2.0−1.1 Å)and an increased splitting between ground state and excited state singly occupied molecular orbitals.
Strongly consistent output only and input/output identification in the presence of Gaussian noise (1991)

Output only and input/output (I/O) system identification algorithms are developed based on a novel mean-square-error (MSE) criterion. The input is assumed non-Gaussian and the performance criterion implicitly exploits cumulant statistics to suppress the effect of additive Gaussian noise. The noise covariance need not be known, and in I/O problems both input and output (perhaps correlated) noises are allowed. Although expressed in terms of noisy data, the novel objective function is a scalar multiple of the standard MSE as if the latter was computed in the absence of noise. It yields strongly consistent parameter estimators which are obtained by solving linear equations via computationally attractive and noise insensitive recursive-least-squares and least-mean-squares algorithms. Simulations illustrate the performance of the proposed algorithms and they are compared with the conventional methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Deep Learning Based OFDM Physical-Layer Receiver for Extreme Mobility (2021)

In this paper, we propose a machine learning (ML) aided physical layer receiver technique for demodulating OFDM signals that are subject to very high Doppler effects and the corresponding distortion in the received signal. Specifically, we develop a deep learning based convolutional neural network receiver system that absorbs proper two-dimensional received signal entities in time and frequency, while containing convolutional neural network layers to efficiently and reliably demodulate the bits — when properly trained — despite the substantial Doppler distortion. Representative set of numerical results is provided, in the context of 5G NR mobile communication network and corresponding base-station demodulation performance for uplink. The obtained results show that the proposed receiver system is able to clearly outperform classical LMMSE receivers that operate on subcarrier level and neglect the Doppler-induced intercarrier interference (ICI). Additionally, the proposed ML receiver has the advantage over ICI cancellation based receivers in terms of the reference signal overhead. This paper provides the description of the method and vast set of numerical results in 5G NR network context.
Kinetics of the Antibody Response to Symptomatic SARS-CoV-2 Infection in Vaccinated and Unvaccinated Individuals in the Blinded Phase of the mRNA-1273 COVID-19 Vaccine Efficacy Trial (2023)

Following COVID-19, vaccinated participants had higher levels and greater breadth of antispike bAbs and higher nAb titers than unvaccinated participants. These were largely attributable to the primary immunization series.
A method for the enzymatic synthesis and HPLC purification of the peptidoglycan precursor UDP-N-acetylmuramic acid (2003)

UDP-N-acetylmuramic acid (UDP-MurNAc) is a precursor for peptidoglycan biosynthesis in bacteria. A major difficulty in the study of this pathway is that UDP-MurNAc is not commercially available. We have developed an enzymatic synthesis scheme for UDP-MurNAc using two easily purified Escherichia coli polyhistidine tagged peptidoglycan biosynthesis enzymes, MurZ and MurB, followed by a single-step purification of UDP-MurNAc by high-performance liquid chromatography. The identity of the UDP-MurNAc synthesized by our method was confirmed by electrospray ionization mass spectrometry. Furthermore, we show that the UDP-MurNAc can support a UDP-MurNAc-L-alanine ligase reaction.