gebhart/patrepeval huggingface dataset:
Clinical Methods: The History, Physical, and Laboratory Examinations (1990)

In these times of burgeoning medical technology and runaway costs, it is a pleasure to find a medical textbook that emphasizes the more basic aspects of practice.<i>Clinical Methods</i>, now in its third edition, reviews the history and physical examination in depth. In addition, the book offers brief discussions of selected laboratory methods used in diagnosis. Compared with previous editions, this volume has undergone extensive revision both in content and organization. Following a brief overview, it is divided into sections based on organ systems. The introductory section includes a useful and well-written chapter on the sensitivity, specificity, and predictive value of laboratory tests, as well as a chapter that takes on the difficult task of articulating the thought processes that are used in the collection and interpretation of medical data. The bulk of the text comprises a detailed discussion of the history and physical examination as related to a particular
Integration architecture of a mobile virtual health record for shared home care. (2005)

The coexistence of different information systems that are unable to communicate with each other is a persistent problem in health care in general, and in shared care in particular. This is especially critical when it comes to information access needed at the point of care, e.g. in the patient's home. The purpose of this paper is to present the technical architecture of a virtual health record (VHR) that both integrates information from different electronic health records (EHRs) and allows for documenting at the point of care using mobile devices. The VHR supports a seamless information and communication flow between different care providers giving them mobile access to selected patient-oriented information. A service oriented system architecture where database functionality and services are separated has been implemented. This guarantees flexibility with regard to changed functional demands and allows third party systems to interact with the platform in a standardised way. Major requirements for the VHR have been documentation support at the point of care, integrated presentation of the information from different feeder systems, and the possibility of offline access to the data on handheld devices. Therefore, publishing was chosen for the integration design. A patient centred XML schema is published as an interface for integration with the information broker. The feeder systems deliver their information in XML.-files that are mapped against the ideal schema and inserted into the mediator database. The paper describes both an online web application and an offline solution that was implemented on personal digital assistants (PDAs). The system has been introduced in a Swedish home care district with an established fiber-optical network infrastructure connecting all the locations forming the study site.
Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM) (2015)

Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/.
Cellular Origin, Tumor Progression, and Pathogenic Mechanisms of Cutaneous Neurofibromas Revealed by Mice with <i>Nf1</i> Knockout in Boundary Cap Cells (2018)

Patients carrying an inactive <i>NF1</i> allele develop tumors of Schwann cell origin called neurofibromas (NF). Genetically engineered mouse models have significantly enriched our understanding of plexiform forms of NFs (pNF). However, this has not been the case for cutaneous neurofibromas (cNF), observed in all NF1 patients, as no previous model recapitulates their development. Here, we show that conditional <i>Nf1</i> inactivation in <i>Prss56</i>-positive boundary cap cells leads to <i>bona fid</i>e pNFs and cNFs. This work identifies subepidermal glia as a likely candidate for the cellular origin of cNFs and provides insights on disease mechanisms, revealing a long, multistep pathologic process in which inflammation-related signals play a pivotal role. This new mouse model is an important asset for future clinical and therapeutic investigations of NF1-associated neurofibromas. SIGNIFICANCE: Patients affected by NF1 develop numerous cNFs. We present a mouse model that faithfully recapitulates cNFs, identify a candidate cell type at their origin, analyze the steps involved in their formation, and show that their development is dramatically accelerated by skin injury. These findings have important clinical/therapeutic implications.<i>This article is highlighted in the In This Issue feature, p. 1</i>.
Predicting stock‐bond correlations (2002)

Refers to previous research on deciding the balance between equities and bonds in investment portfolios and puts forward a model based on a single period correlation to predict future stock‐bond correlations from past interest and growth rates. Explains the concepts involved and uses 1948‐2000 US data to test it. Shows that the model predicts stock‐bond correlation significantly better than the traditional method of extrapolating from past correlations; and relates this to the theory of loanable funds. Concludes that high interest rates and high growth lead to higher correlations between stocks and bonds and calls for further research.
An algebraic parameter estimation approach to the adaptive observer-controller based regulation of the boost converter (2007)

In this article, a new approach is proposed for the problem of output voltage reference trajectory tracking in a boost converter with unknown, piecewise constant, load resistance values, under the restriction of noisy output voltage measurements alone. We use a nonlinear algebraic parameter estimation approach for the fast computation of the actual value of the stepwise changing load. With this information, a reduced order nonlinear observer for the inductor current is updated as well as a static passive output feedback control law derived on the basis of the exact tracking error dynamics and Lyapunov stability considerations. The average nonlinear adaptive observer-controller scheme is implemented on the switch regulated converter using the averaging features of a Σ -Δ modulator.
GI-core polymer optical waveguide for triggering the migration of optical interconnects from inter-rack to PCBs (2014)

We introduce GI-core polymer waveguides as a promising component for triggering the migration of optical interconnects from Inter-racks to PCBs in data-center networks. We spotlight “the Mosquito method” that we developed for simultaneous fabrication and integration for GI-core polymer waveguides on-board.
Two Round Multiparty Computation via Multi-Key FHE (2015)

We construct a general multiparty computation MPC protocol with only two rounds of interaction in the common random string model, which is known to be optimal. In the honest-but-curious setting we only rely on the learning with errors LWE assumption, and in the fully malicious setting we additionally assume the existence of non-interactive zero knowledge arguments NIZKs. Previously, Asharov et al. EUROCRYPT '12 showed how to achieve three rounds based on LWE and NIZKs, while Garg et al. TCC '14 showed how to achieve the optimal two rounds based on indistinguishability obfuscation, but it was unknown if two rounds were possible under standard assumptions without obfuscation.

Our approach relies on multi-key fully homomorphic encryption MFHE, introduced by Lopez-Alt et al. STOC '12, which enables homomorphic computation over data encrypted under different keys. We present a construction of MFHE based on LWE that significantly simplifies a recent scheme of Clear and McGoldrick CRYPTO '15. We then extend this construction to allow for a one-round distributed decryption of a multi-key ciphertext. Our entire MPC protocol consists of the following two rounds:1.Each party individually encrypts its input under its own key and broadcasts the ciphertext. All parties can then homomorphically compute a multi-key encryption of the output.2.Each party broadcasts a partial decryption of the output using its secret key. The partial decryptions can be combined to recover the output in plaintext.
Posttraumatic Stress Disorder: An Immunological Disorder? (2017)

Patients with posttraumatic stress disorder (PTSD) exhibit an increased state of inflammation. Various animal models for PTSD have shown some of the same immune imbalances as have been shown in human subjects with PTSD, and some of these studies are discussed in this review. However, animal studies can only indirectly implicate immune involvement in PTSD in humans. This review of mainly studies with human subjects focuses on dissecting the immunological role in the pathogenesis of PTSD following initial trauma exposure. It addresses both the inflammatory state associated with PTSD and the immune imbalance between stimulatory and inhibitory immune mediators, as well as variables that can lead to discrepancies between analyses. The concept of immunological treatment approaches is proposed for PTSD, as new treatments are needed for this devastating disorder that is affecting unprecedented numbers of Veterans from the long-standing wars in the Middle East and which affects civilians following severe trauma.
Racial and gender differences in N-acetyltransferase, xanthine oxidase, and CYP1A2* activities (1992)

Racial and gender differences in xanthine oxidase activity render the AFMU/1X ratio less reliable as an assessment of NAT activity in a heterogeneous population compared with the AFMU/(1U + 1X) or AFMU/(AFMU + 1U + 1X) ratios. The observed racial and gender differences in NAT, xanthine oxidase, and CYP1A2 activities may have implications for racial and gender differences in drug effects and carcinogen biotransformation.
Database semantics representation for natural language access (2003)

In natural language database interfaces (NLDBI), manual construction of translation knowledge normally undermines domain portability because of its expensive human intervention. To overcome this, this paper proposes linguistically-motivated database semantics in order to systematically construct translation knowledge. Database semantics consists of two structures which are designed to function as a translation dictionary, and to contain selectional restriction constraints on domain classes. The database semantics is semi-automatically obtained from a semantic data model for a target database. Based on this database semantics, a conceptual NLDBI translation scheme is developed. Translating a natural language question into a database query suffers from the translation ambiguity problem, which has not received significant attention in this field. To deal with translation ambiguity, we suggest an ambiguity resolution method based on the proposed database semantics. Experiments showed the usefulness of the proposed database semantics and its disambiguation procedures.
Screening Mangrove Endophytic Fungi for Antimalarial Natural Products (2013)

We conducted a screening campaign to investigate fungi as a source for new antimalarial compounds. A subset of our fungal collection comprising Chinese mangrove endophytes provided over 5000 lipophilic extracts. We developed an accelerated discovery program based on small-scale cultivation for crude extract screening and a high-throughput malaria assay. Criteria for hits were developed and high priority hits were subjected to scale-up cultivation. Extracts from large scale cultivation were fractionated and these fractions subjected to both in vitro malaria and cytotoxicity screening. Criteria for advancing fractions to purification were developed, including the introduction of a selectivity index and by dereplication of known metabolites. From the Chinese mangrove endophytes, four new compounds (14-16, 18) were isolated including a new dimeric tetrahydroxanthone, dicerandrol D (14), which was found to display the most favorable bioactivity profile.
Sponge-Based Control-Flow Protection for IoT Devices (2018)

Embedded devices in the Internet of Things (IoT) face a wide variety of security challenges. For example, software attackers perform code injection and code-reuse attacks on their remote interfaces, and physical access to IoT devices allows to tamper with code in memory, steal confidential Intellectual Property (IP), or mount fault attacks to manipulate a CPU's control flow. In this work, we present Sponge-based Control Flow Protection (SCFP). SCFP is a stateful, sponge-based scheme to ensure the confidentiality of software IP and its authentic execution on IoT devices. At compile time, SCFP encrypts and authenticates software with instruction-level granularity. During execution, an SCFP hardware extension between the CPU's fetch and decode stage continuously decrypts and authenticates instructions. Sponge-based authenticated encryption in SCFP yields fine-grained control-flow integrity and thus prevents code-reuse, code-injection, and fault attacks on the code and the control flow. In addition, SCFP withstands any modification of software in memory. For evaluation, we extended a RISC-V core with SCFP and fabricated a real System on Chip (SoC). The average overhead in code size and execution time of SCFP on this design is 19.8% and 9.1 %, respectively, and thus meets the requirements of embedded IoT devices.
Poliovirus Polyuridylic Acid Polymerase and RNA Replicase Have the Same Viral Polypeptide (1979)

A poliovirus-specific polyuridylic acid [poly(U)] polymerase that copies a polyadenylic acid template complexed to an oligouridylic acid primer was isolated from the membrane fraction of infected HeLa cells and was found to sediment at 4 to 5S on a linear 5 to 20% glycerol gradient. When the poly(U) polymerase was isolated from cells labeled with [(35)S]methionine and was analyzed by glycerol gradient centrifugation and polyacrylamide gel electrophoresis, the position of only one viral protein was found to correlate with the location of enzyme activity. This protein had an apparent molecular weight of 62,500 based on its electrophoretic mobility relative to that of several molecular weight standards and was designated p63. When the poly(U) polymerase was isolated from the soluble fraction of a cytoplasmic extract, the activity was found to sediment at about 7S. In this case, however, both p63 and NCVP2 (77,000-dalton precursor of p63) cosedimented with the 7S activity peak. When the 7S polymerase activity was purified by phosphocellulose chromatography, both p63 and NCVP2 were found to co-chromatograph with poly(U) polymerase activity. The poliovirus replicase complexed with its endogenous RNA template was isolated from infected cells labeled with [(35)S]methionine and was centrifuged through a linear 15 to 30% glycerol gradient. The major viral polypeptide component in a 26S peak of replicase activity was p63, but small amounts of other poliovirus proteins were also present. When the replicase-template complex was treated with RNase T1 before centrifugation, a single peak of activity was found that sedimented at 20S and contained only labeled p63. Thus, p63 was found to be the only viral polypeptide in the replicase bound to its endogenous RNA template, and appears to be active as a poly(U) polymerase either as a monomer protein or as a 7S complex.
A mining algorithm based on time series association rules (2012)

Based on the concept lattice theory, this paper studies the cycle of association rule mining about the periodic fluctuations of time-series. First of all, do anti-season pretreatment to time-series, then give the algorithm of the generation of the cycle of association rules, and the pruning to the generated concept within algorithm improve the efficiency of the mining speed. And then we can use the given higher precision model to do anti-season changes calculation to those time series which dissatisfy anti-season pretreatment using the moving average method.
High-Dimensional Design-Of-Experiments Extracts Small-Molecule-Only Induction Conditions for Dorsal Pancreatic Endoderm from Pluripotency (2020)

The derivation of endoderm and descendant organs, such as pancreas, liver, and intestine, impacts disease modeling and regenerative medicine. Use of TGF-β signaling agonism is a common method for induction of definitive endoderm from pluripotency. By using a data-driven, High-Dimensional Design of Experiments (HD-DoE)-based methodology to address multifactorial problems in directed differentiation, we found instead that optimal conditions demanded BMP antagonism and retinoid input leading to induction of dorsal foregut endoderm (DFE). We demonstrate that pancreatic identity can be rapidly, and robustly, induced from DFE and that such cells are of dorsal pancreatic identity. The DFE population was highly competent to differentiate into both stomach organoids and pancreatic tissue types and able to generate fetal-type β cells through two subsequent differentiation steps using only small molecules. This alternative, rapid, and low-cost basis for generating pancreatic insulin-producing cells may have impact for the development of cell-based therapies for diabetes.
Large‐scale prediction of protein geometry and stability changes for arbitrary single point mutations (2004)

We have developed a method to both predict the geometry and the relative stability of point mutants that may be used for arbitrary mutations. The geometry optimization procedure was first tested on a new benchmark of 2141 ordered pairs of X-ray crystal structures of proteins that differ by a single point mutation, the largest data set to date. An empirical energy function, which includes terms representing the energy contributions of the folded and denatured proteins and uses the predicted mutant side chain conformation, was fit to a training set consisting of half of a diverse set of 1816 experimental stability values for single point mutations in 81 different proteins. The data included a substantial number of small to large residue mutations not considered by previous prediction studies. After removing 22 (approximately 2%) outliers, the stability calculation gave a standard deviation of 1.08 kcal/mol with a correlation coefficient of 0.82. The prediction method was then tested on the remaining half of the experimental data, giving a standard deviation of 1.10 kcal/mol and covariance of 0.66 for 97% of the test set. A regression fit of the energy function to a subset of 137 mutants, for which both native and mutant structures were available, gave a prediction error comparable to that for the complete training set with predicted side chain conformations. We found that about half of the variation is due to conformation-independent residue contributions. Finally, a fit to the experimental stability data using these residue parameters exclusively suggests guidelines for improving protein stability in the absence of detailed structure information.
Optics damage modeling and analysis at the National Ignition Facility (2014)

Comprehensive modeling of laser-induced damage in optics for the National Ignition Facility (NIF) has been performed on fused silica wedge focus lenses with a metric that compares the modeled damage performance to online inspections. The results indicate that damage models are successful in tracking the performance of the fused silica final optics when properly accounting for various optical finishes and mitigation processes. This validates the consistency of the damage models and allows us to further monitor and evaluate different system parameters that potentially can affect optics performance.
Specific HDAC6 inhibition by ACY-738 reduces SLE pathogenesis in NZB/W mice (THER6P.858) (2014)

Abstract Histone deacetylase inhibitors are important modifiers of gene and protein expression. In our studies, we sought to determine if a specific HDAC6 inhibitor (ACY-738) was able to decrease disease in NZB/W lupus-prone mice through regulation of B and T cell differentiation. From 22 - 38 weeks-of-age, NZB/W mice were injected intraperitoneally with 20 mg/kg of ACY-738, 5 mg/kg of ACY-738, or DMSO (vehicle control). Body weight and proteinuria were measured every 2 weeks, while sera anti-dsDNA, Ig isotypes, and cytokine levels were measured every 4 weeks. Kidney disease was determined using sera and urinary markers of SLE, immune complex deposition, and renal pathology. Flow cytometric analysis was used to assess thymic and splenic T cell profiles as well as bone marrow, splenic, and peripheral B cell differentiation patterns. Our results showed that HDAC6 inhibition was able to decrease many hallmarks of SLE disease including splenomegaly, immune complex-mediated glomerulonephritis, sera anti-dsDNA levels, and inflammatory cytokine production. ACY-738 treatment decreased the number of double-negative thymic T cells and increased the percentage of splenic Treg cells. Inhibition of HDAC6 altered BM B cell differentiation by increasing the percentage of cells in the early-stage developmental fractions of both pro-and pre-B cells. These results suggest that specific HDAC6 inhibition may be able to decrease SLE disease by altering aberrant T and B cell differentiation.
Sub-pT magnetic field detection by tunnel magneto-resistive sensors (2021)

Abstract We developed tunnel magneto-resistive (TMR) sensors based on magnetic tunnel junctions (MTJs) that are able to detect a weak, sub-pT, magnetic field at a low frequency. Small detectivities of 0.94 pT/Hz 1/2 at 1 Hz and 0.05 pT/Hz 1/2 at 1 kHz were achieved by lowering the resistance of MTJs and enhancement of the signal using a thick CoFeSiB layer and magnetic flux concentrators. We demonstrated real-time measurement of magnetocardiography (MCG) and nuclear magnetic resonance (NMR) of protons using developed sensors. This result shows that both MCG and NMR can be measured by the same measurement system with ultra-sensitive TMR sensors.
Product Differentiation Alternatives: Identity Preservation, Segregation, and Traceability (2002)

There is growing evidence that face recognition is "special" but less certainty concerning the way in which it is special. The authors review and compare previous proposals and their own more recent hypothesis, that faces are recognized "holistically" (i.e., using relatively less part decomposition than other types of objects). This hypothesis, which can account for a variety of data from experiments on face memory, was tested with 4 new experiments on face perception. A selective attention paradigm and a masking paradigm were used to compare the perception of faces with the perception of inverted faces, words, and houses. Evidence was found of relatively less part-based shape representation for faces. The literatures on machine vision and single unit recording in monkey temporal cortex are also reviewed for converging evidence on face representation. The neuropsychological literature is reviewed for-evidence on the question of whether face representation differs in degree or kind from the representation of other types of objects.