gebhart/patrepeval huggingface dataset:
Red Bus Lane Treatment Evaluation (2012)

The New York City Department of Transportation (NYCDOT) has implemented red-colored bus lanes as part of its collaborative Bus Rapid Transit (BRT) program with MTA New York City Transit (NYCT) since 2008. NYCDOT and NYCT have found that the red treatment is effective at reducing unauthorized bus lane usage. NYCDOT is seeking to improve the durability and cost-effectiveness of its preferred red lane treatment. In 2010 a research study began to identify high performance red lane products and installation processes for different roadway surfaces. This paper will present the methodologies and findings from a series of field and laboratory tests used to evaluate red bus lane treatments for NYCDOT. The field evaluations included long-term observations of various products used on bus-only lanes, as well as durability and skid resistance testing. Parallel laboratory evaluations were also undertaken to assess product durability and skid resistance in a controlled, indoor laboratory. The results indicate that a red epoxy-based street paint, an epoxy with red aggregate product, and a red asphalt concrete-based micro surface performed well across all field and laboratory tests.
Linguistically inspired roadmap for building biologically reliable protein language models (2022)

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM approaches do not contribute to a fundamental understanding of sequence-function mappings, hindering rule-based biotherapeutic drug development. We argue that guidance drawn from linguistics, a field specialized in analytical rule extraction from natural language data, can aid with building more interpretable protein LMs that are more likely to learn relevant domain-specific rules. Differences between protein sequence data and linguistic sequence data require the integration of more domain-specific knowledge in protein LMs compared to natural language LMs. Here, we provide a linguistics-based roadmap for protein LM pipeline choices with regard to training data, tokenization, token embedding, sequence embedding, and model interpretation. Incorporating linguistic ideas into protein LMs enables the development of next-generation interpretable machine-learning models with the potential of uncovering the biological mechanisms underlying sequence-function relationships.
Forest microclimate dynamics drive plant responses to warming (2020)

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilization). Species responses often lag behind climate warming, but the reasons for such lags remain largely unknown. Here, we analyzed multidecadal understory microclimate dynamics in European forests and show that thermophilization and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased local heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes.
Verifiable annotations for embedded java environments (2005)

Many implementations of Java Virtual Machine (JVM) use optimizing dynamic compilation for improving performance of Java applications. However, optimizing compilation is expensive in terms of both time and memory space complexity. Annotations are frequently used to reduce the dynamic compilation overhead in embedded Java environments where the memory budget and CPU speed are limited. However, some annotations can cause the dynamic compiler to generate code that violates the security policy of the JVM. These annotations present a safety problem if they are not verified before being used by the compiler. In this work, we present annotation schemes for three frequently used optimizations: null pointer check removal, value liveness analysis, and array bound check removal. All our annotations can be verified at low cost during dynamic compilation time to guarantee that they do not cause the compiler to generate code that violates the security policy of the JVM.
Antiviral Enantiomeric Preference for 5'-Noraristeromycin (1994)

In order to determine if the potent antiviral properties of (+/-)-5'-noraristeromycin reside in one of its enantiomers, an analysis of each enantiomer has been carried out. A five-step route to the (+)-stereoisomer is described from (+)-(1R,4S)-4-hydroxy-2-cyclopenten-1-yl acetate, whereas the synthesis of the (-)-enantiomer had been reported previously from the same starting material. The (-)-2 and (+)-2 enantiomers were evaluated for antiviral activity against a large number of viruses and found to display an antiviral activity spectrum characteristic of (S)-adenosyl-L-homocysteine hydrolase inhibitors. The (-)-enantiomer retained the significant anticytomegalovirus properties previously reported for the racemic 2 and was, on the average, 10-fold more potent than (+)-2 in inhibiting virus replication, tumor cell growth, and (S)-adenosyl-L-homocysteine hydrolase activity.
The GEO 600 gravitational wave detector (2002)

The GEO 600 laser interferometer with 600 m armlength is part of a worldwide network of gravitational wave detectors. Due to the use of advanced technologies like multiple pendulum suspensions with a monolithic last stage and signal recycling, the anticipated sensitivity of GEO 600 is close to the initial sensitivity of detectors with several kilometres armlength. This paper describes the subsystems of GEO 600, the status of the detector by September 2001 and the plans towards the first science run.
Activated vitamin D3 formulations can be safely used as concomitant medication for prevention of denosumab‐induced hypocalcemia in women with postmenopausal osteoporosis (2019)

This study indicates that the use of activated vitamin D preparations, as concomitant medications with denosumab therapy, is appropriate considering the therapeutic efficacy of denosumab, prevention of hypocalcemia, and influence on renal function.
Joint Detection of Human and Object Motion Using Harmonic Micro-Doppler Radar and Harmonic Tags (2020)

We present a new method for jointly detecting the motion of moving people and tagged objects using harmonic micro-Doppler radar and passive harmonic tags. Wirelessly measuring the motion of people and held objects is important for applications, including sensing in living spaces and industrial monitoring. A significant challenge in discriminating the motion of objects from that of people is the relatively low signal power generated by the radar return from a held object relative to the clutter return power. We overcome this limitation by using harmonic tags that generate a response at a harmonic of the incident radar signal. The radar emits a continuous-wave (CW) signal at a fundamental frequency of 2.5 GHz, which scatters off the person and is collected by a 2.5 GHz receiver. The harmonic tag collects the 2.5 GHz signal and generates a harmonic response at 5 GHz, which is collected by a 5 GHz receiver on the radar. Frequency modulation on the 5 GHz signal is thus generated only by the motion of the tag, while the 2.5 GHz modulation is predominantly due to the motion of the person. The fundamental and harmonic received signals can thus be processed separately for direct joint detection of the dynamic motion of people and held objects.
Laser Pulse Phenomena and Applications (2010)

Pulsed lasers are available in the gas, liquid, and the solid state. These lasers are also enormously versatile in their output characteristics yielding emission from very large energy pulses to very high peak-power pulses. Pulsed lasers are equally versatile in their spectral characteristics. This volume includes an impressive array of current research on pulsed laser phenomena and applications. <em>Laser Pulse Phenomena and Applications</em> covers a wide range of topics from laser powered orbital launchers, and laser rocket engines, to laser-matter interactions, detector and sensor laser technology, laser ablation, and biological applications.
Randomized T rial o f B lack C ohosh f or t he T reatment o f Hot F lashes A mong W omen W ith a H istory o f Breast C ancer (2001)

Purpose: Most breast cancer survivors experience hot flashes; many use complementary or alternative remedies for these symptoms. We undertook a randomized clinical trial of black cohosh, a widely used herbal remedy for menopausal symptoms, among breast cancer patients. Patients and Methods: Patients diagnosed with breast cancer who had completed their primary treatment were randomly assigned to black cohosh or placebo, stratified on tamoxifen use. At enrollment, patients completed a questionnaire about demographic factors and menopausal symptoms. Before starting to take the pills and at 30 and 60 days, they completed a 4-day hot flash diary. At the final visit, they completed another menopausal symptom questionnaire. Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels were measured in a subset of patients at the first and final visits. Results: Of 85 patients (59 on tamoxifen, 26 not on tamoxifen) enrolled in the study, 42 were assigned to treatment and 43 were assigned to placebo; 69 completed all three hot flash diaries. Both treatment and placebo groups reported declines in number and intensity of hot flashes; the differences between the groups were not statistically significant. Both groups also reported improvements in menopausal symptoms that were, for the most part, not significantly different. Changes in blood levels of FSH and LH also did not differ in the two groups. Conclusion: Black cohosh was not significantly more efficacious than placebo against most menopausal symptoms, including number and intensity of hot flashes. Our study illustrates the feasibility and value of standard clinical trial methodology in assessing the efficacy and safety of herbal agents. J Clin Oncol 19:2739-2745. © 2001 by American Society of Clinical Oncology.
AlN/h-BN Heterostructures for Mg Dopant-Free Deep Ultraviolet Photonics (2017)

Aluminum-rich AlGaN is the ideal material system for emerging solid-state deep-ultraviolet (DUV) light sources. Devices operating in the near-UV spectral range have been realized; to date, however, the achievement of high-efficiency light-emitting diodes (LEDs) operating in the UV-C band (200-280 nm specifically) has been hindered by the extremely inefficient p-type conduction in AlGaN and the lack of DUV-transparent conductive electrodes. Here, we show that these critical challenges can be addressed by Mg dopant-free Al(Ga)N/h-BN nanowire heterostructures. By exploiting the acceptor-like boron vacancy formation, we have demonstrated that h-BN can function as a highly conductive, DUV-transparent electrode; the hole concentration is ∼10<sup>20</sup> cm<sup>-3</sup> at room temperature, which is 10 orders of magnitude higher than that previously measured for Mg-doped AlN epilayers. We have further demonstrated the first Al(Ga)N/h-BN LED, which exhibits strong emission at ∼210 nm. This work also reports the first achievement of Mg-free III-nitride LEDs that can exhibit high electrical efficiency (80% at 20 A/cm<sup>2</sup>).
Somatic Hypermethylation of MSH2 Is a Frequent Event in Lynch Syndrome Colorectal Cancers (2010)

Heritable germline epimutations in MSH2 have been reported in a few Lynch syndrome families that lacked germline mutations in the MSH2 gene. It is not known whether somatic MSH2 methylation occurs in MSH2 mutation-positive Lynch syndrome subjects or sporadic colorectal cancers (CRC). Therefore, we determined the methylation status of the MSH2 gene in 268 CRC tissues, including 222 sporadic CRCs and 46 Lynch syndrome tumors that did not express MSH2. We also looked for microsatellite instability (MSI), germline mutations in the MSH2 and EpCAM genes, somatic mutations in BRAF and KRAS, and the CpG island methylator phenotype (CIMP). We observed that somatic MSH2 hypermethylation was present in 24% (11 of 46) of MSH2-deficient (presumed Lynch syndrome) tumors, whereas no evidence for MSH2 methylation existed in sporadic CRCs (MSI and microsatellite stable) or normal colonic tissues. Seven of 11 (63%) patients with MSH2 methylation harbored simultaneous pathogenic germline mutations in the MSH2 gene. Germline EpCAM deletions were present in three of four patients with MSH2 methylation but without pathogenic MSH2 germline mutations. The mean methylation scores at CIMP-related markers were significantly higher in Lynch syndrome tumors with MSH2 methylation than MSH2-unmethylated CRCs. In conclusion, our data provide evidence for frequent MSH2 hypermethylation in Lynch syndrome tumors with MSH2 deficiency. MSH2 methylation in this subset of individuals is somatic and may serve as the "second hit" at the wild-type allele. High levels of aberrant methylation at CIMP-related markers in MSH2-methylated tumors raise the possibility that MSH2 is a target susceptible to aberrant methylation in Lynch syndrome.
Ultramicroscopy: Light-Sheet-Based Microscopy for Imaging Centimeter-Sized Objects with Micrometer Resolution (2013)

Ultramicroscopy (UM) is a powerful imaging technique that achieves precise and accurate three-dimensional (3D) reconstructions of intact macroscopic specimens with micrometer resolution. It was developed for specimens in the size range of ∼1-15 mm, such as whole mouse brains, mouse embryos, mouse organs, and Drosophila melanogaster. In UM, the specimen is illuminated perpendicular to the observation pathway by two thin counterpropagating sheets of laser light. UM is closely related to a growing family of comparable microscopy approaches based on light sheet illumination developed in recent years. This article presents an overview of light-sheet-based microscopy and describes the underlying physics of light sheet generation. The assembly of an "ultramicroscope" for investigating fixed chemically cleared tissue is described in detail, and the functions of the essential components, such as mechanics, camera, and objectives, are discussed. Finally, practical applications of UM for studying mouse organs, mouse embryos, and Drosophila adults are described.
Age-Related Loss of Ciliary Muscle Mobility in the Rhesus Monkey (1992)

Ciliary muscle topography was studied in rhesus monkey eyes (aged 6 to 29 years) bisected meridionally through cornea and optic nerve head. Half of each eye was incubated in atropine sulfate, the other in pilocarpine hydrochloride, and both were then processed for histologic study. Several ciliary muscle sections from the original cut margin and the middle of the half eyes were traced and compared quantitatively. In sections from the middle, where the attachments of the muscle were presumably intact, the pilocarpine effect on ciliary muscle topography was lost with age. In sections near the cut margin, where some of the posterior attachments were disrupted and the choroid had detached from the sclera, the pilocarpine effect persisted with age. These findings suggest that loss of ciliary muscle movement with age is caused by decreased compliance of its posterior attachment.
Wanted Dead or Alive: A Correlate of Protection Against Dengue Virus (2019)

OPINION article Front. Immunol., 16 December 2019Sec. Viral Immunology Volume 10 - 2019 | https://doi.org/10.3389/fimmu.2019.02946
MeV Multiple Implantation of Nitrogen Ions to Pure Chromium. II. Effect of Heat Treatment on the Depth Profile of Nitrogen Concentration. (1992)

Polycrystalline chromium metal plates (purity>99.99%) were implanted with nitrogen ions (N2+) at energies of 500keV, 1MeV, 1.5MeV and 2MeV and the doses of from 3×1017 to 1×1018N atoms/cm2. The implanted chromium plates were annealed repeatedly at varying temperatures from 250°C to 800°C. The depth profiles of nitrogen concentration was investigated by Rutherford Backscattering Spectrometry (RBS) and the crystallinity of the nitride layer was studied by XRD. At temperatures up to 400-500°C, CrN converted to Cr2N and phase transition were observed. However, the amorphous nature of the nitride layer formed was kept after annealing. The maximum Cr2N layer thickness of obtained by multiple implantation (2MeV-1.5MeV-1MeV, total=2.1·1018) and subsequent annealing was 650nm (from 200nm to 850nm in depth scale).
Loss of heterochromatin and retrotransposon silencing as determinants in oocyte aging (2022)

Mammalian oocyte quality reduces with age. We show that prior to the occurrence of significant aneuploidy (9M in mouse), heterochromatin histone marks are lost, and oocyte maturation is impaired. This loss occurs in both constitutive and facultative heterochromatin marks but not in euchromatic active marks. We show that heterochromatin loss with age also occurs in human prophase I-arrested oocytes. Moreover, heterochromatin loss is accompanied in mouse oocytes by an increase in RNA processing and associated with an elevation in L1 and IAP retrotransposon expression and in DNA damage and DNA repair proteins nuclear localization. Artificial inhibition of the heterochromatin machinery in young oocytes causes an elevation in retrotransposon expression and oocyte maturation defects. Inhibiting retrotransposon reverse-transcriptase through azidothymidine (AZT) treatment in older oocytes partially rescues their maturation defects and activity of the DNA repair machinery. Moreover, activating the heterochromatin machinery via treatment with the SIRT1 activating molecule SRT-1720, or overexpression of Sirt1 or Ezh2 via plasmid electroporation into older oocytes causes an upregulation in constitutive heterochromatin, downregulation of retrotransposon expression, and elevated maturation rates. Collectively, our work demonstrates a significant process in oocyte aging, characterized by the loss of heterochromatin-associated chromatin marks and activation of specific retrotransposons, which cause DNA damage and impair oocyte maturation.
Localization of nerve growth factor (NGF) and low‐affinity NGF receptors in touch domes and quantification of NGF mRNA in keratinocytes of adult rats (1994)

Touch domes are clearly delineated mechanoreceptors that are visible on the depilated skin of mammals. These structures consist of a sharply circumscribed disk of thickened epithelium surmounting a group of Merkel cells that are innervated by type I sensory neurons. These characteristic cutaneous structures provide an ideal opportunity for investigating whether the localization of nerve growth factor (NGF) in the skin is related to sites of sensory axon termination. For these reasons, we have used immunocytochemistry to study the distribution of NGF and the low-affinity NGF receptor (p75NGFR) in the touch domes of adult rat skin. Intense NGF-like immunoreactivity was sharply restricted to keratinocytes (excluding the stratum corneum) of the thickened epidermis of touch domes. The epidermis immediately surrounding touch domes and the epidermis of the tylotrich hair follicle associated with touch domes were not stained by anti-NGF antiserum. Merkel cells of the basal epidermis of touch domes were immunonegative for NGF but were immunopositive for p75NGFR as were the type I nerve endings innervating these cells. Quantitative Northern blotting revealed that the level of NGF mRNA was substantially higher in keratinocytes isolated from the stratum granulosum and stratum spinosum than in keratinocytes isolated from the stratum germinativum. These findings indicate that NGF synthesis in mature skin has a highly restricted regional distribution that is primarily associated with the innervation of a specialized touch receptor.
Structure−Property Relationships for Two-Photon Absorbing Chromophores:  Bis-Donor Diphenylpolyene and Bis(styryl)benzene Derivatives (2000)

The two-photon absorption properties of a series of bis dialkylamino- or diarylamino-substituted diphenylpolyenes and bis(styryl)benzenes have been investigated. Two-photon absorption cross sections, δ, as large as 1420 × 10-50 cm4 s/photon-molecule have been observed for molecules with this general bis-donor structure. The effect of the type and length of the conjugated chain and of dialkylamino or diarylamino substitution on the position and magnitude of the peak two-photon absorptivity is reported. The transition dipole moments for the transitions between the ground state and the first excited singlet state (Mge) and between the first and second excited singlet states (Mee‘) have been estimated using experimental data from the one- and two-photon spectra. It was found that increases in chain length result mainly in an increase in Mge, whereas the addition of donor end groups or going from diphenylpolyene- to phenylene-vinylene-type bridges leads primarily to an increase in Mee‘. The trends in the energy of the lowest excited singlet states and in the transition moments for the diphenylpolyene series as a function of chain length are in agreement with those calculated by quantum mechanical methods. These results furnish a link between structural features in these classes of molecules and the electronic dipole couplings and state energies that control the strength of the two-photon absorption. In bis(aminophenyl)polyenes containing up to four double bonds (m) the lowest excited singlet state is a Bu state, as opposed to the case of simple polyenes and diphenylpolyenes, for which it is an Ag state for m > 2. The relationship of the state ordering in these systems with the observed values of the radiative and nonradiative decay rates is also discussed.
Psychological Sequelae of Torture and Trauma in Chilean and Salvadorean Migrants: A Pilot Study (1995)

Torture has existed since the earliest times, usually as public punishment prior to death. Today it is predominantly used in secret with the aim of destroying the individual's personality. The effects of torture include severe physical and psychological sequelae which have only recently come under scrutiny. In recent years many Chilean and El Salvadorean migrants have left their countries after being tortured and severely traumatised as a result of organised violence. The aim of this study was to pilot an investigation into the psychological sequelae of torture. Subjects were 30 Chileans and El Salvadoreans classified into three groups: torture, trauma and non-torture/trauma migrants. It was found to be feasible to access and interview survivors from a clinical research perspective without causing additional psychological morbidity. The subjects were interviewed and administered three scales: the Post-Traumatic Stress Disorder Scale, SCL-90-R, and the Impact of Event Scale. The results from the scales and the descriptive data presented indicate some support for the hypothesis that torture survivors show higher levels of PTSD, psychosomatic impairment and stress response disturbance than the trauma and non-torture/trauma groups. Methodological issues are discussed. The strengths and limitations of this preliminary study are considered in relation to future research.
Mandarin Lexical Tone Acquisition in Cochlear Implant Users With Prelingual Deafness: A Review (2016)

Despite the demonstrated limitations of pitch perception in cochlear implant users, there is some evidence that typical production and perception of lexical tone is possible by cochlear implant users with prelingual deafness. Further studies are required to determine the factors that contribute to better outcomes to inform rehabilitation processes for cochlear implant users in tonal-language environments.