gebhart/patrepeval huggingface dataset:
Theoretical Determination of Activation Free Energies for Alkaline Hydrolysis of Cyclic and Acyclic Phosphodiesters in Aqueous Solution (2004)

First-principles electronic structure calculations were performed in this study to examine the reaction pathway and corresponding activation free energies for alkaline hydrolysis of representative phosphodiesters, including dimethyl phosphate (DMP), trimethylene phosphate (TMP), ethylene phosphate (EP), and a simplified model (cAMPm) of adenosine 3‘, 5‘-phosphate (cAMP). Reaction coordinate calculations show that for all of these phosphodiesters the alkaline hydrolysis follows a one-step bimolecular mechanism initialized by the attack of hydroxide ion at the phosphorus atom of the ester. Five self-consistent reaction field (SCRF) methods were used to calculate the activation free energies and the calculated results were compared with available experimental data. It has been shown that the results calculated using a recently developed SCRF method, known as the surface and volume polarization for electrostatics (SVPE) or fully polarizable continuum model (FPCM), which accurately determines both surface and volume polarization, are rather insensitive to the used solute charge isodensity contour value that determines the solute cavity size. The SVPE calculations plus nonelectrostatic interaction corrections led to activation free energies 32.6, 31.6, 24.8, and 29.4 kcal/mol for DMP, TMP, EP, and cAMPm, respectively. The calculated activation free energies are all in good agreement with available experimentally estimated activation free energies ∼32, ∼32, ∼21−24, and ∼29 kcal/mol for DMP, TMP, EP, and cAMP, respectively. The SVPE results show that the solvation dramatically decreases the activation free energies for the alkaline hydrolysis of phosphodiesters and strongly support the conclusion that the remarkable difference in the hydrolysis rate between DMP and EP is mainly due to the solvation, rather than the ring-strain. Compared to the SVPE results and available experimental data, an SCRF method that completely ignores volume polarization systematically overestimated the activation free energies, but the relative values of the calculated activation free energies are still in qualitative agreement with those of the SVPE results and available experimental data. The other three SCRF methods using a certain charge renormalization scheme also overestimated the activation free energies, and the relative values of the calculated activation free energies are all significantly different from those of the SVPE results and available experimental data.
d -Lactate Dehydrogenase Gene ( ldhD ) Inactivation and Resulting Metabolic Effects in the Lactobacillus johnsonii Strains La1 and N312 (1999)

Lactobacillus johnsonii La1, a probiotic bacterium with demonstrated health effects, grows in milk, where it ferments lactose to D- and L-lactate in a 60:40% ratio. The D-lactate dehydrogenase (D-LDH) gene (ldhD) of this strain was isolated, and an in vitro-truncated copy of that gene was used to inactivate the genomic copy in two strains, La1 and N312, by gene replacement. For that, an 8-bp deletion was generated within the cloned ldhD gene to inactivate its function. The plasmid containing the altered ldhD was transferred to L. johnsonii via conjugative comobilization with Lactococcus lactis carrying pAMbeta1. Crossover integrations of the plasmid at the genomic ldhD site were selected, and appropriate resolution of the cointegrate structures resulted in mutants that had lost the plasmid and in which the original ldhD was replaced by the truncated copy. These mutants completely lacked D-LDH activity. Nevertheless, the lower remaining L-LDH activity of the cells was sufficient to reroute most of the accumulating pyruvate to L-lactate. Only a marginal increase in production of the secondary end products acetaldehyde, diacetyl, and acetoin was observed. It can be concluded that in L. johnsonii D- and L-LDH are present in substantial excess for their role to eliminate pyruvate and regenerate NAD(+) and that accumulated pyruvate is therefore not easily redirected in high amounts to secondary metabolic routes.
APPLYING RFID TECHNOLOGY TO DEVELOP A DISTANT MEDICAL CARE SERVICE PLATFORM (2010)

With the increasing number of elderly people in modern society, the market of medical care is emerging and has dramatically increased in recent years. However, there is yet little research focused on developing a service platform for distant medical care. Hence, this research attempts to apply radio frequency identification (RFID) technology to develop a distant medical care service platform (DMCSP) to support home-based medical care. The DMCSP functions include modules like: situation monitoring, diagnosis, prognosis, inventory management, and service scheduling and dispatching. To describe the proposed DMCSP clearly, this study applies Unified Modeling Language (UML) as a tool to clarify the system analysis and design. Finally, the differences between the as-is model and the to-be model of medical care for the elderly are demonstrated for emphasizing the efficiency and effectiveness of home-based distant medical care service.
Novel Insights into Siderophore Formation in Myxobacteria (2005)

The myxochelins are catecholate-type siderophores produced by a number of myxobacterial strains, and their corresponding biosynthetic gene clusters have been identified in Stigmatella aurantiaca Sg a15, and Sorangium cellulosum So ce56; the latter being presented in this work. Biochemical and genetic studies described here further clarify myxochelin biosynthesis. In addition to the myxochelin A biosynthetic complex, the aminotransferase MxcL is required in order to form myxochelin B, starting from 2,3-dihydroxy benzoic acid and L-lysine. Additionally, the substrate specificity of the myxochelin A biosynthetic complex was analyzed in vitro; this led to the formation of novel myxochelin derivatives. Furthermore, MxcD was over-expressed and its function as an active isochorismic acid synthase in Escherichia coli was verified by complementation studies, as was activity in vitro. The organization of the myxochelin gene cluster of S. cellulosum So ce56 was compared to that of the Sg a15 gene cluster. The comparison revealed that although the organization of the biosynthetic genes is completely different, the biosynthesis is most probably extremely similar.
Definition of Fiducial Points in the Normal Seismocardiogram (2018)

The purpose of this work is to define fiducial points in the seismocardiogram (SCG) and to correlate them with physiological events identified in ultrasound images. For 45 healthy subjects the SCG and the electrocardiogram (ECG) were recorded simultaneously at rest. Immediately following the SCG and ECG recordings ultrasound images of the heart were also obtained at rest. For all subjects a mean SCG signal was calculated and all fiducial points (peaks and valleys) were identified and labeled in the same way across all signals. Eight physiologic events, including the valve openings and closings, were annotated from ultrasound as well and the fiducial points were correlated with those physiologic events. A total of 42 SCG signals were used in the data analysis. The smallest mean differences (±SD) between the eight events found in the ultrasound images and the fiducial points, together with their correlation coefficients (r) were: atrial systolic onset: -2 (±16) ms, r = 0.75 (p < 0.001); peak atrial inflow: 13 (±19) ms, r = 0.63 (p < 0.001); mitral valve closure: 4 (±11) ms, r = 0.71 (p < 0.01); aortic valve opening: -3 (±11) ms, r = 0.60 (p < 0.001); peak systolic inflow: 13 (±23) ms, r = 0.42 (p < 0.01); aortic valve closure: -5 (±12) ms, r = 0.94 (p < 0.001); mitral valve opening: -7 (±19) ms, r = 0.87 (p < 0.001) and peak early ventricular filling: -18 (±28 ms), r = 0.79 (p < 0.001). In conclusion eight physiologic events characterizeing the cardiac cycle, are associated with reproducible, well-defined fiducial points in the SCG.
Transfer-learning for differentiating epileptic patients who respond to treatment based on chronic ambulatory ECoG data (2019)

The aim of this study was to evaluate whether transfer-learning with pre-trained deep convolutional neural networks (deep CNNs) can be used for assessing patient outcomes in epilepsy. Transfer-learning with the GoogLeNet InceptionV3 CNN model pre-trained on the large ImageNet dataset (~1.2 million images) was able to differentiate upper (n=12) and lower (n=9) response quartile mesiotemporal lobe epilepsy patients in the NeuroPace <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> RNS <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> System clinical trials with ~76% classification accuracy based on chronic ambulatory baseline electrocorticographic (ECoG) data. These promising findings justify further research using deep CNNs for assessing patient outcomes in epilepsy.
Articular Cartilage Injuries (2002)

The acute and repetitive impact and torsional joint loading that occurs during participation in sports can damage articular surfaces causing pain, joint dysfunction, and effusions. In some instances, this articular surface damage leads to progressive joint degeneration. Three classes of chondral and osteochondral injuries can be identified based on the type of tissue damage and the repair response: (1) damage to the joint surface that does not cause visible mechanical disruption of the articular surface, but does cause chondral damage and may cause subchondral bone injury; (2) mechanical disruption of the articular surface limited to articular cartilage; and (3) mechanical disruption of articular cartilage and subchondral bone. In most instances, joints can repair damage that does not disrupt the articular surface if they are protected from additional injury. Mechanical disruption of articular cartilage stimulates chondrocyte synthetic activity, but it rarely results in repair of the injury. Disruption of subchondral bone stimulates chondral and bony repair, but it rarely restores an articular surface that duplicates the biologic and mechanical properties of normal articular cartilage. In selected patients, surgeons have used operative treatments including penetrating subchondral bone, soft tissue grafts, and cell transplants and osteochondral autografts and allografts to restore articular surfaces after chondral injuries. Experimental studies indicate that use of artificial matrices and growth factors also may promote formation of a new joint surface. However, an operative treatment of an articular surface injury that will benefit patients must not just provide a new joint surface, it must produce better long-term joint function than would be expected if the injury was left untreated or treated by irrigation and debridement alone. Therefore, before selecting a treatment for a patient with an articular cartilage injury, the surgeon should define the type of injury and understand its likely natural history.
Identification and Characterization of a Peptide That Specifically Binds the Human, Broadly Neutralizing Anti-Human Immunodeficiency Virus Type 1 Antibody b12 (2001)

Human monoclonal antibody (MAb) b12 recognizes a conformational epitope that overlaps the CD-4-binding site of the human immunodeficiency virus type 1 (HIV-1) envelope. MAb b12 neutralizes a broad range of HIV-1 primary isolates and protects against primary virus challenge in animal models. We report here the discovery and characterization of B2.1, a peptide that binds specifically to MAb b12. B2.1 was selected from a phage-displayed peptide library by using immunoglobulin G1 b12 as the selecting agent. The peptide is a homodimer whose activity depends on an intact disulfide bridge joining its polypeptide chains. Competition studies with gp120 indicate that B2.1 occupies the b12 antigen-binding site. The affinity of b12 for B2.1 depends on the form in which the peptide is presented; b12 binds best to the homodimer as a recombinant polypeptide fused to the phage coat. Originally, b12 was isolated from a phage-displayed Fab library constructed from the bone marrow of an HIV-1-infected donor. The B2.1 peptide is highly specific for b12 since it selected only phage bearing b12 Fab from this large and diverse antibody library.
The Histone Methyltransferase Activity of MLL1 Is Dispensable for Hematopoiesis and Leukemogenesis (2014)

Despite correlations between histone methyltransferase (HMT) activity and gene regulation, direct evidence that HMT activity is responsible for gene activation is sparse. We address the role of the HMT activity for MLL1, a histone H3 lysine 4 (H3K4) methyltransferase critical for maintaining hematopoietic stem cells (HSCs). Here, we show that the SET domain, and thus HMT activity of MLL1, is dispensable for maintaining HSCs and supporting leukemogenesis driven by the MLL-AF9 fusion oncoprotein. Upon Mll1 deletion, histone H4 lysine 16 (H4K16) acetylation is selectively depleted at MLL1 target genes in conjunction with reduced transcription. Surprisingly, inhibition of SIRT1 is sufficient to prevent the loss of H4K16 acetylation and the reduction in MLL1 target gene expression. Thus, recruited MOF activity, and not the intrinsic HMT activity of MLL1, is central for the maintenance of HSC target genes. In addition, this work reveals a role for SIRT1 in opposing MLL1 function.
A Four-Step Diastereoselective Synthesis of D-erythro-Sphingosine by an Enantioselective Aldol Reaction Using a Titanium Enolate Derived from a Chiral Iminoglycinate (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Four-Step Diastereoselective Synthesis of D-erythro-Sphingosine by an Enantioselective Aldol Reaction Using a Titanium Enolate Derived from a Chiral IminoglycinateArlette Solladie-Cavallo and Jean L. KoesslerCite this: J. Org. Chem. 1994, 59, 11, 3240–3242Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://pubs.acs.org/doi/10.1021/jo00090a052https://doi.org/10.1021/jo00090a052research-articleACS PublicationsRequest reuse permissionsArticle Views665Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Pim kinases phosphorylate multiple sites on Bad and promote 14-3-3 binding and dissociation from Bcl-XL (2006)

All three Pim kinase family members predominantly phosphorylate Bad on Ser112 and in addition are capable of phosphorylating Bad on multiple sites associated with the inhibition of the pro-apoptotic function of Bad in HEK-293 cells. This would be consistent with the proposed function of Pim kinases in promoting cell proliferation and preventing cell death.
A Systematic Approach to Design an Efficient Physical Unclonable Function (2012)

A Physical Unclonable Function (PUF) has shown a lot of promise to solve many security issues due to its ability to generate a random yet chip-unique secret in the form of an identifier or a key while resisting cloning attempts as well as physical tampering. It is a hardware-based challenge-response function which maps its responses to its challenges exploiting complex statistical variation in the logic and interconnect inside integrated circuits (ICs). An efficient PUF should generate a key that varies randomly from one chip to another. At the same time, it should reliably reproduce a key from a chip every time the key is requested from that chip. Moreover, a PUF should be robust to thwart any attack that aims to reveal its key. Designing an efficient PUF having all these qualities with a low cost is challenging. Furthermore, the efficiency of a PUF needs to be validated by characterizing it over a group of chips. This is because a PUF circuit is supposed to be instantiated in several chips, and whether it can produce a chip-unique identifier/key or not cannot be validated using a single chip. The main goal of this research is to propose a systematic approach to build a random, reliable, and robust PUF incurring minimal cost. With this objective, we first formulate a novel PUF system model that uncouples PUF
Isomagnetophoresis to Discriminate Subtle Difference in Magnetic Susceptibility (2007)

We report an improved magnetophoretic method, isomagnetophoresis, employing the magnetic susceptibility gradient across a microfluidic channel applied by magnetic field, and we have successfully discriminated the polystyrene (PS; 14.78 ?? 0.20 ??m in diameter), poly(methyl methacrylate) (PMMA; 15.00 ?? 0.77 ??m) and borosilicate (BS; 14.01 ?? 1.00 ??m) microspheres, where PS and PMMA particles have similar diamagnetic susceptibility that cannot be distinguished by conventional magnetophoresis. This platform can be applied to label-free discrimination of the biological cells and nanotubes.
Non-HFE haemochromatosis (2007)

Non-HFE hereditary haemochromatosis (HH) refers to a genetically heterogeneous group of iron overload disorders that are unlinked to mutations in the HFE gene. The four main types of non-HFE HH are caused by mutations in the hemojuvelin, hepcidin, transferrin receptor 2 and ferroportin genes. Juvenile haemochromatosis is an autosomal recessive disorder and can be caused by mutations in either hemojuvelin or hepcidin. An adult onset form of HH similar to HFE-HH is caused by homozygosity for mutations in transferrin receptor 2. The autosomal dominant iron overload disorder ferroportin disease is caused by mutations in the iron exporter ferroportin. The clinical characteristics and molecular basis of the various types of non-HFE haemochromatosis are reviewed. The study of these disorders and the molecules involved has been invaluable in improving our understanding of the mechanisms involved in the regulation of iron metabolism.
Full duplex radios (2013)

This paper presents the design and implementation of the first in-band full duplex WiFi radios that can simultaneously transmit and receive on the same channel using standard WiFi 802.11ac PHYs and achieves close to the theoretical doubling of throughput in all practical deployment scenarios. Our design uses a single antenna for simultaneous TX/RX (i.e., the same resources as a standard half duplex system). We also propose novel analog and digital cancellation techniques that cancel the self interference to the receiver noise floor, and therefore ensure that there is no degradation to the received signal. We prototype our design by building our own analog circuit boards and integrating them with a fully WiFi-PHY compatible software radio implementation. We show experimentally that our design works robustly in noisy indoor environments, and provides close to the expected theoretical doubling of throughput in practice.
FDA-approved poly(ethylene glycol)–protein conjugate drugs (2011)

PEGylation or covalent attachment of poly(ethylene glycol) improves the pharmacokinetic properties of protein drugs. In vivo circulation lifetimes are increased and dosages are decreased, resulting in improved patient quality of life. PEG may be attached to proteins using a variety of different chemical reactions. This review discusses currently available FDA-approved PEGylated protein drugs, their intended use and target, and the PEG attachment chemistry utilized.
NM 01. Feed access effect on body growth, carcass and internal organs of two strains of broilers (1997)

The objective of this paper was to evaluate the yield and corporal composition of two commercial strains of broilers at four slaughter ages with different daily times. Birds were 208 ISA Vedette (ISA) strain, and 208 Arbor Acres (AA) strain, feed a starter diet (23 % CP) up to the 36 days and a grower diet(21 %CP) up to the end of the experience. There were random samples assigned to three times of daily feeding: 24, 9 and 7 hours, with 2, 3 and 3 replicates respectively for each strain x feed schedule. Four random sample chicks for each pen were slaughtered at 16, 32, 46 and 56 days old, with the measuring of the folowing weights: Live weight (PV), eviscerated carcass weight (PC), abdominal fat (GA), feathers (PL), small intestine (ID), large intestine (IG), gizzard (M), proventriculus (EG), liver(H) and heart(C). Data were analized by the GLM procedures of SAS. In any case measures were affected by the strain factor (P>.05). Only in PV, PC and GA 7 and 9 had significantly differences (P
Molecular weight of the photoprotein aequorin (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleMolecular weight of the photoprotein aequorinY. Kohama, O. Shimomura, and F. H. JohnsonCite this: Biochemistry 1971, 10, 22, 4149–4152Publication Date (Print):October 1, 1971Publication History Published online1 May 2002Published inissue 1 October 1971https://pubs.acs.org/doi/10.1021/bi00798a022https://doi.org/10.1021/bi00798a022research-articleACS PublicationsRequest reuse permissionsArticle Views148Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Polymeric bound porphyrins and their precursors, 6. Syntheses of water‐soluble, negatively or un‐charged polymers with covalently bound moieties of porphyrin derivatives (1988)

Abstract Water‐soluble polymers 6 – 17 containing covalently bound moieties of porphyrin derivatives were prepared by reaction of poly(methacrylic acid) ( 4 ) and poly( N ‐vinylpyrrolidone‐ co ‐methacrylic acid) ( 5 ) with the low‐molecular‐weight substituted tetraphenylporphyrin 1 b , phthalocyanines 2 b and 2 d and naphthocyanine 3 c . Besides binding of one porphyrin derivative, also combined binding of two or three different porphyrin derivatives to the polymers could be achieved. The resulting polymers are negatively charged (polymers 6 – 11 ) or uncharged (polymers 12 – 17 ).