gebhart/patrepeval huggingface dataset:
It Seems Like Only Yesterday (2015)

I spent my childhood and adolescence in North and South Carolina, attended Duke University, and then entered Duke Medical School. One year in the laboratory of George Schwert in the biochemistry department kindled my interest in biochemistry. After one year of residency on the medical service of Duke Hospital, chaired by Eugene Stead, I joined the group of Arthur Kornberg at Stanford Medical School as a postdoctoral fellow. Two years later I accepted a faculty position at Harvard Medical School, where I remain today. During these 50 years, together with an outstanding group of students, postdoctoral fellows, and collaborators, I have pursued studies on DNA replication. I have experienced the excitement of discovering a number of important enzymes in DNA replication that, in turn, triggered an interest in the dynamics of a replisome. My associations with industry have been stimulating and fostered new friendships. I could not have chosen a better career.
Selective growth of sculptured nanowires on microlithographic lattices (2004)

We have grown helicoidal nanowire assemblies on a variety of topographic substrates with regular microlithographic patterns, thereby demonstrating that sculptured thin films with transversely latticed architecture can be grown by physical vapor deposition. The transverse feature-separations are as low as 100–300 nm, and mesa regions are circular posts as small as 60 nm in diameter. The initial as well as the subsequent stages of growth on topographic substrates can be understood using simple geometric shadowing arguments.
Using real‐time MRI to quantify altered joint kinematics in subjects with patellofemoral pain and to evaluate the effects of a patellar brace or sleeve on joint motion (2008)

Abnormal patellofemoral joint motion is a possible cause of patellofemoral pain, and patellar braces are thought to alleviate pain by restoring normal joint kinematics. We evaluated whether females with patellofemoral pain exhibit abnormal patellofemoral joint kinematics during dynamic, weight-bearing knee extension and assessed the effects of knee braces on patellofemoral motion. Real-time magnetic resonance (MR) images of the patellofemoral joints of 36 female volunteers (13 pain-free controls, 23 patellofemoral pain) were acquired during weight-bearing knee extension. Pain subjects were also imaged while wearing a patellar-stabilizing brace and a patellar sleeve. We measured axial-plane kinematics from the images. Females with patellofemoral pain exhibited increased lateral translation of the patella for knee flexion angles between 0 degrees and 50 degrees (p = 0.03), and increased lateral tilt for knee flexion angles between 0 degrees and 20 degrees (p = 0.04). The brace and sleeve reduced the lateral translation of the patella; however, the brace reduced lateral displacement more than the sleeve (p = 0.006). The brace reduced patellar tilt near full extension (p = 0.001), while the sleeve had no effect on patellar tilt. Our results indicate that some subjects with patellofemoral pain exhibit abnormal weight-bearing joint kinematics and that braces may be effective in reducing patellar maltracking in these subjects.
Base-catalyzed isomerization of retinoic acid. Synthesis and differentiation-inducing activities of 14-alkylated all-trans-, 13-cis-, and 20,14-retro-retinoic acids (1992)

Retinoic acid (1) is isomerized regioselectively by excess amounts of lithium diisopropylamide (LDA) to give 20,14-retro-retinoic acid (3). Alkylation of the intermediate dianion of retinoic acid gave 14-alkylated derivatives of 3. By isomerization of the alkylated retro isomers under basic conditions, several 14-alkyl-all-trans- and -13-cis-retinoic acids were synthesized. The retinoidal activities of these derivatives were examined, based on the ability to induce differentiation of human promyelocytic leukemia cell line HL-60. 20,14-retro-Retinoic acid (3) is 1/50 as active as retinoic acid (1). Although 14-methyl-20,14-retro-retinoic acid (4) is as active as 3, the introduction of a 14-methyl group into all-trans- and 13-cis-retinoic acid resulted in decreased activity. Introduction of bulkier alkyl groups at the C-14 position caused the disappearance of the activity.
Long-Term Follow-Up of Patients with Obscure Gastrointestinal Bleeding After Negative Capsule Endoscopy (2006)

Patients with OGIB and negative CE had a very low rebleeding rate, and further invasive investigations can be deferred.
Beyond ketonization: selective conversion of carboxylic acids to olefins over balanced Lewis acid–base pairs (2016)

We report the direct conversion of mixed carboxylic acids to C-C olefins with up to 60 mol% carbon yield through cascade (cross) ketonization, (cross) aldolization and self-deoxygenation reactions. Co-feeding hydrogen provides an additional ketone hydrogenation/dehydration pathway to a wider range of olefins.
Effect of celecoxib on experimental liver fibrosis in rat (2005)

Celecoxib potentiates experimental liver fibrosis; further studies are warranted to investigate the potential pro-fibrogenic effect of celecoxib in other animal models of liver fibrosis and in patients with chronic hepatitis.
Towards a realistic in vitro experience of epidural Tuohy needle insertion (2013)

The amount of pressure exerted on the syringe and the depth of needle insertion are the two key factors for successfully carrying out epidural procedure. The force feedback from the syringe plunger is helpful in judging the loss of pressure, and the depth of the needle insertion is crucial in identifying when the needle is precisely placed in the epidural space. This article presents the development of two novel wireless devices to measure these parameters to precisely guide the needle placement in the epidural space. These techniques can be directly used on patients or implemented in a simulator for improving the safety of procedure. A pilot trial has been conducted to collect depth and pressure data with the devices on a porcine cadaver. These measurements are then combined to accurately configure a haptic device for creating a realistic in vitro experience of epidural needle insertion.
Electrochemically active threading intercalator with high double stranded DNA selectivity (1998)

A naphthalene diimide threading intercalator carrying ferrocenyl moieties as its termini can discriminate double stranded DNA from single stranded counterparts owing to a difference in their dissociation rates.
Asymptotic waveform evaluation for transient analysis of 3-D interconnect structures (1993)

An approach to computing the time response of an arbitrary 3-D interconnect structure based on asymptotic waveform evaluation (AWE) is introduced. It has been implemented in a software tool called 3DAWE. To facilitate the application of AWE to a 3D RC mesh network model, the AWE formulation is rederived based on a nodal analysis approach. The ICCG matrix solver has been successfully applied in 3DAWE. It is shown that the typical transient response of a reasonably large 3D RC network can be obtained within a few minutes on a 15-MIPS computer using this program.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract 4022: ERK1/2 inhibitor ulixertinib demonstrates activity in atypical (non-V600) BRAF mutant models (2022)

Abstract Atypical BRAF (non-V600) alterations comprise approximately half of all BRAF mutations in cancer and can be categorized according to characteristics of molecular signaling (either Class II or III). Atypical BRAF alterations are rare (approximately 3% across all human cancers) and there are currently no approved therapies for this indication. As next-generation sequencing becomes standard clinical practice, oncologists are frequently identifying atypical BRAF alterations in their patients’ tumors. The efficacy of the first-in-class ERK1/2 inhibitor, ulixertinib (BVD-523), was assessed across 10 patient-derived xenograft (PDX) models, which harbored class II or III BRAF alterations (5 models with type II alterations, 4 models with class III, and 1 model with both class II and III). Responses ranging from robust regression to moderate tumor growth delay were observed in 9/10 models. RNA sequencing was performed on tumors from the vehicle-treated and ulixertinib-treated groups with three replicates per PDX model. The samples were collected 2 hours after the last dose of treatment. Expression of the mutant BRAF alleles was readily confirmed from RNA-seq data in all PDX models. In addition, gene expression analysis showed differential expression of MAPK pathway genes in responders compared to the non-responders. In summary, ulixertinib has exhibited strong pre-clinical activity in a variety of patient-derived xenograft models with atypical BRAF alterations. Ulixertinib has FDA fast-track designation for patients with solid tumors, other than CRC, harboring specific BRAF mutations (G469A, L485W, or L597Q) and is currently under clinical evaluation in patients with tumors harboring any atypical BRAF alteration (NCT04488003). Citation Format: Deborah Knoerzer, Anupama Reddy, Adnan Derti, Caroline M. Emery. ERK1/2 inhibitor ulixertinib demonstrates activity in atypical (non-V600) BRAF mutant models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4022.
Molecular Determinants of West Nile Virus Virulence and Pathogenesis in Vertebrate and Invertebrate Hosts (2020)

West Nile virus (WNV), like the dengue virus (DENV) and yellow fever virus (YFV), are major arboviruses belonging to the <i>Flavivirus</i> genus. WNV is emerging or endemic in many countries around the world, affecting humans and other vertebrates. Since 1999, it has been considered to be a major public and veterinary health problem, causing diverse pathologies, ranging from a mild febrile state to severe neurological damage and death. WNV is transmitted in a bird-mosquito-bird cycle, and can occasionally infect humans and horses, both highly susceptible to the virus but considered dead-end hosts. Many studies have investigated the molecular determinants of WNV virulence, mainly with the ultimate objective of guiding vaccine development. Several vaccines are used in horses in different parts of the world, but there are no licensed WNV vaccines for humans, suggesting the need for greater understanding of the molecular determinants of virulence and antigenicity in different hosts. Owing to technical and economic considerations, WNV virulence factors have essentially been studied in rodent models, and the results cannot always be transported to mosquito vectors or to avian hosts. In this review, the known molecular determinants of WNV virulence, according to invertebrate (mosquitoes) or vertebrate hosts (mammalian and avian), are presented and discussed. This overview will highlight the differences and similarities found between WNV hosts and models, to provide a foundation for the prediction and anticipation of WNV re-emergence and its risk of global spread.
Reply to Spek and Duitman (2023)

"Reply to: PCSK6: The endogenous PAR-1 agonist driving pulmonary fibrosis?." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
GMPLS RSVP-TE Extensions for SONET/SDH and OTN OAM Configuration (2013)

GMPLS has been extended to support connection establishment in both
SONET/SDH and OTN networks. However support for the configuration of
the OAM functions is not specified. Both SONET/SDH and OTN implement
OAM functions to monitor the transported signals. This document
defines extensions to RSVP-TE for SONET/SDH and OTN OAM configuration
based on the OAM Configuration Framework defined in a separate
document. This document supports, but does not modify, ITU-T OAM
mechanisms.
Functional Optical Coherence Tomography in Preclinical Models (2011)

Functional imaging is a powerful tool for investigating biological signaling, disease processes, and potential therapies in both in vivo and in vitro systems. Microscopy, including confocal and multiphoton microscopy, has been the standard for high-resolution functional imaging in live cells and tissues. However, these microscopy techniques suer from relatively shallow imaging depths. Magnetic resonance imaging (MRI) and PET have been the standard for functional imaging deep within the body, with the caveat of relatively poor resolution. Optical coherence tomography (OCT) lls a niche between high-resolution microscopy techniques and whole-body imaging techniques with relatively good resolution (∼1-10 μm) and penetration depths (∼1-2 mm) in tissue. OCT thus provides structural information noninvasively in vivo at a resolution similar to that of histology. Combined functional and structural imaging in this regime could become a powerful tool for small animal studies.
A DNA origami plasmonic sensor with environment-independent read-out (2019)

DNA origami is a promising technology for its reproducibility, flexibility, scalability and biocompatibility. Among the several potential applications, DNA origami has been proposed as a tool for drug delivery and as a contrast agent, since a conformational change upon specific target interaction may be used to release a drug or produce a physical signal, respectively. However, its conformation should be robust with respect to the properties of the medium in which either the recognition or the read-out take place, such as pressure, viscosity and any other unspecific interaction other than the desired target recognition. Here we report on the read-out robustness of a tetragonal DNA-origami/gold-nanoparticle hybrid structure able to change its configuration, which is transduced in a change of its plasmonic properties, upon interaction with a specific DNA target. We investigated its response when analyzed in three different media: aqueous solution, solid support and viscous gel. We show that, once a conformational variation is produced, it remains unaffected by the subsequent physical interactions with the environment.
Mokko Lactone Alleviates Doxorubicin-Induced Cardiotoxicity in Rats via Antioxidant, Anti-Inflammatory, and Antiapoptotic Activities (2022)

Doxorubicin (DOX), a commonly utilized anthracycline antibiotic, suffers deleterious side effects such as cardiotoxicity. Mokko lactone (ML) is a naturally occurring guainolide sesquiterpene with established antioxidant and anti-inflammatory actions. This study aimed at investigating the protective effects of ML in a DOX-induced cardiotoxicity model in rats. Our results indicated that ML exerted protection against cardiotoxicity induced by DOX as indicated by ameliorating the rise in serum troponin and creatine kinase-MB levels and lactate dehydrogenase activity. Histological assessment showed that ML provided protection against pathological alterations in heart architecture. Furthermore, treatment with ML significantly ameliorated DOX-induced accumulation of malondialdehyde and protein carbonyl, depletion of glutathione, and exhaustion of superoxide dismutase and catalase. ML’s antioxidant effects were accompanied by increased nuclear translocation of NF-E2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) expression. Moreover, ML exhibited significant anti-inflammatory activities as evidenced by lowered nuclear factor κB, interleukin-6, and tumor necrosis factor-α expression. ML also caused significant antiapoptotic actions manifested by modulation in mRNA expression of Bax, Bcl-2, and caspase-3. This suggests that ML prevents heart injury induced by DOX via its antioxidant, anti-inflammatory, and antiapoptotic activities.
Sandia Photonics Technology for Avionics (2007)

Since its inception, Sandia National Laboratories has developed and fielded a wide variety of components and systems for many challenging applications. Avionics-related optoelectronics R&D is a core capability of Sandia. This paper will review activity in vertical-cavity surface-emitting lasers (VCSEL), micro-electromechanical systems (MEMS) and photonic-integrated circuits (PICs) as applied to various applications including built-in fiber diagnostics, beam forming and RF data links
Conserved sequence homology of cysteine-rich regions in genes encoding glycoprotein A in Pneumocystis carinii derived from different host species (1994)

Pneumocystis carinii surface glycoprotein A (gpA) exhibits host species-specific phenotypic and genotypic variation. Despite this heterogeneity, the gpAs of P. carinii isolated from different host species appear to be homologous molecules sharing certain biochemical and antigenic characteristics. Using two degenerate oligodeoxyribonucleotide primers corresponding to conserved cysteine regions from ferret and rat P. carinii gpAs, a PCR product of approximately 300 bp was amplified from ferret, rat, and SCID mouse P. carinii-infected lung genomic DNA. Northern (RNA) hybridization revealed a transcript of 3,450 nucleotides in P. carinii-infected SCID mouse lung mRNA, which is similar in size to the transcripts for ferret and rat P. carinii gpAs. Nucleotide sequence analysis of SCID mouse P. carinii gpA subclones derived from the PCR products identified two isoforms, which were 89% identical to each other in the amplified region and 73 and 54% identical to the rat- and ferret-derived P. carinii gpA genes, respectively. Comparison of the deduced amino acid sequences of mouse, ferret, and rat P. carinii gpAs revealed striking similarity in residues adjacent to and including the conserved cysteines. Furthermore, the spacing of two proline residues is invariant, and a potential N-linked glycosylation site is found at a similar position in all of the gpAs. Despite the heterogeneity observed in P. carinii gpAs, the conservation of cysteine residues and adjacent sequences implies similar secondary structure and, most likely, similar function for the gpAs of P. carinii isolated from different host species.
Towards non-invasive high-resolution 3D nano-tomography by ultrasonic scanning probe microscopy (2017)

Nanoscale imaging techniques that can be used to visualize and characterize local aggregations of the embedded nanoparticulates with sufficient resolution have attracted a great deal of interest. Ultrasonic scanning probe microscopy (SPM) and its derivatives are nondestructive techniques that can be used to elucidate subsurface nanoscale features and mechanical properties. Although many different ultrasonic methods have been used for subsurface imaging, the mechanisms and crucial parameters associated with the contrast formation in subsurface imaging are still unclear. Here, the impact of mechanical properties of the nanoparticulates/matrix, size of the nanoparticulates, buried depth of the nanoparticulates, and the ultrasonic excitation frequency on the developed ultrasonic SPM images have been investigated. To verify our theoretical model, experimental measurements of scanning near-field ultrasound holography (SNFUH) have been recreated in our theoretical analysis to reveal comparable variations in phase contrast measured in SNFUH while scanning over the nanoparticulates embedded in bacteria.
Local Modifications of Single-Wall Carbon Nanotubes Induced by Bond Formation with Encapsulated Fullerenes (2007)

Defected fullerenes in nanopeapods form bonds with the encapsulating single-walled carbon nanotubes when irradiated by an electron beam leading to changes in the guest (fullerene) and the host (nanotube). Intrinsic reaction coordinate (IRC) analysis based on B3LYP hybrid density functional theory shows that a C1-C59 defect with a single protruding C atom is initially formed from the C60(Ih) cage. The high activation energy for this step (8.37 eV (193.0 kcal/mol)), being assumed to be accessible during irradiation, is lower than that of the Stone-Wales rearrangement on the sp2 network. The binding of the defected fullerene to the nanotube is preferential, orthogonal bonds relative to the tube axis being slightly preferred. Because of the covalent bonds formed between the guest and host, the carbon network on the nanotube is locally perturbed in the vicinity of the binding site. As a result of the new bonds, bisnorcaradiene-like as well as quinonoid-like patterns appear near the binding site. These results are interpreted using orbital interaction and Clar diagram arguments. The changes in the bonding pattern on the nanotube should be significant in further functionalization of carbon nanotubes.
Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum (2014)

The expression profiles, co-expression networks and co-expression regulation of the 10 tissues studied and the tissue-specific analysis presented here are a valuable resource for studying tissue-specific biological functions in nematodes.
Donor sex, pre‐donation hemoglobin, and manufacturing affect CD71+cells in red cell concentrates (2023)

RCCs have variable numbers of CD71<sup>+</sup> RBCs. This makes understanding the impact of donor factors and manufacturing methods on the immunomodulatory effect of CD71<sup>+</sup> RBCs critical in exploring donor-recipient sex-mismatched transfusions.
On the Applicability of Single-Walled Carbon Nanotubes as VLSI Interconnects (2009)

This paper presents a comprehensive study of the applicability of single-walled carbon nanotubes (SWCNTs) as interconnects in nanoscale integrated circuits. A detailed analysis of SWCNT interconnect resistance (considering its dependence on all physical parameters, as well as factors affecting the contact resistance), the first full 3-D capacitance simulations of SWCNT bundles for realistic very large scale integration (VLSI) interconnect dimensions, and a quantitative evaluation of the importance of inductive effects in SWCNT interconnects are presented. The applicability of carbon nanotube (CNT) based vias (vertical interconnects)-the most realizable CNT interconnects in the current state of the art-is addressed for the first time. It is shown that CNT interconnects can provide 30%-40% improvement in the delay of millimeter-long global interconnects. The applicability of CNT monolayers as local interconnects is found to be much more limited than that reported in the prior literature. Dense CNT bundle global interconnects are shown to offer a 4times reduction in power dissipation while achieving the same delay as optimally buffered Cu interconnects at the 22 nm node. This power saving increases to 8times at the 14 nm node. Furthermore, 3-D finite-element electrothermal simulations show that CNT bundles used as vias in between Cu metal layers can provide large improvement in metal interconnect lifetime by lowering the temperature of the hottest interconnects.
Imprint of gravitational waves in models dominated by a dynamical cosmic scalar field (1998)

An alternative to the standard cold dark matter model has been recently proposed in which a significant fraction of the energy density of the universe is due to a dynamical scalar field $(Q)$ whose effective equation of state differs from that of matter, radiation or cosmological constant $(\ensuremath{\Lambda}).$ In this paper, we determine how the $Q$ component modifies the primordial inflation gravitational wave (tensor metric) contribution to the cosmic microwave background anisotropy and, thereby, one of the key tests of inflation.