gebhart/patrepeval huggingface dataset:
Genetic analysis of a streptomycin-resistant oligosporogenous Bacillus subtilis mutant (1984)

Strain SRB15T+, a streptomycin-resistant, oligosporogenous mutant of Bacillus subtilis, contains two mutations, fun and strR. These mutations were mapped by PBS-1 mediated transduction and by transformation to two different sites in the cysA-linked region of the B. subtilis chromosome. The fun mutation mapped very close to rpsLl, a classic strA mutation, whereas strR mapped to a site distal to rpsE. The effects of these mutations on growth, sporulation, and streptomycin resistance in vivo and in vitro were determined. The fun mutation gave a different phenotype than did the rpsLl mutation and caused altered migration of a ribosomal protein which was identified as S12, the protein encoded by rpsL. It therefore appears that fun is an allele of the rpsL gene.
ChemInform Abstract: Comparison of Solution and Solid State Structure of 2,3‐ Dihydrobenzofuran Derivatives (I). Part 7. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Induction of Terminal Differentiation Markers by the cAMP Pathway in Human HaCaT Keratinocytes (1998)

The terminal differentiation of human epidermal keratinocytes is a complex morphological and biochemical shift from a mitotically active cell to an inert protein cross-linked envelope. This transition is a clearly predetermined cell death mechanism, but it is unlike many other programmed cell deaths in that it is not apoptotic. To explore and contrast the mechanism by which keratinocytes are committed to differentiation rather than apoptosis, we focused on the cyclic adenosine monophosphate (cAMP) signaling pathway using selective modulators of intracellular cAMP levels. Markers of differentiation were assayed by Western blotting. Raising intracelluar cAMP levels by treating HaCaT cells with forskolin, a diterpene, or with isobutylmethylxanthine, a phosphodiesterase inhibitor, and isoproterenol, a beta-adrenergic receptor agonist that selectively activates adenylate cyclase, increased the levels of the differentiation markers keratin K1 and K10, involucrin and transglutaminase. H89 and KT5720, both inhibitors of cAMP-dependent protein kinase, suppressed the expression of keratins K1 and K10. These observations are in line with the defined role for cAMP in the control of keratinocyte differentiation.
Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls (2017)

Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotton stems are compositionally very different from that reported for other plant species, including Arabidopsis. The current definition of a 'typical' primary or secondary cell wall might not be applicable to all cell types in all plant species.
Improved Integrated Robotic Intraocular Snake: Analyses of the Kinematics and Drive Mechanism of the Dexterous Distal Unit (2021)

Retinal surgery can be performed only by surgeons possessing advanced surgical skills because of the small, confined intraocular space, and the restricted free motion of the instruments in contact with the sclera. Snake-like robots may be essential for use in retinal surgery to overcome this problem. Such robots can approach the target site from suitable directions and operate on delicate tissues during retinal vein cannulation, epiretinal membrane peeling, and so on. We propose an improved integrated robotic intraocular snake (I<sup>2</sup>RIS), which is a new version of our previous IRIS. This study focused on the analyses of the kinematics and drive mechanism of the dexterous distal unit. This unit consists of small elements with reduced contact stress achieved by changing wire-hole positions. The kinematic analysis of the dexterous distal unit shows that it is possible to control the bending angle and direction of the unit by using two pairs of drive wires. The proposed drive mechanism includes a new pull-and-release wire mechanism in which the drive pulley is mounted at a right angle relative to the actuation direction (also, relative to the conventional direction). Analysis of the drive mechanism shows that compared to the previous drive mechanism, the proposed mechanism is simpler and easier to assemble and yields higher accuracy and resolution. Furthermore, considering clinical use, the instrument of the I<sup>2</sup>RIS is detachable from the motor unit easily for cleaning, sterilization, and attachment of various surgical tools. Analyses of the kinematics and drive mechanism and the basic functions of the proposed mechanism were verified experimentally on actual-size prototypes of the instrument and motor units.
AES-CCM Cipher Suites for Transport Layer Security (TLS) (2012)

This memo describes the use of the Advanced Encryption Standard (AES)
in the Counter with Cipher Block Chaining - Message Authentication
Code (CBC-MAC) Mode (CCM) of operation within Transport Layer Security
(TLS) and Datagram TLS (DTLS) to provide confidentiality and data
origin authentication. The AES-CCM algorithm is amenable to compact
implementations, making it suitable for constrained environments.
[STANDARDS-TRACK]
Distinct hormonal and morphological control of dormancy and germination in Chenopodium album dimorphic seeds (2023)

Dormancy and heteromorphism are innate seed properties that control germination timing through adaptation to the prevailing environment. The degree of variation in dormancy depth within a seed population differs considerably depending on the genotype and maternal environment. Dormancy is therefore a key trait of annual weeds to time seedling emergence across seasons. Seed heteromorphism, the production of distinct seed morphs (in color, mass or other morphological characteristics) on the same individual plant, is considered to be a bet-hedging strategy in unpredictable environments. Heteromorphic species evolved independently in several plant families and the distinct seed morphs provide an additional degree of variation. Here we conducted a comparative morphological and molecular analysis of the dimorphic seeds (black and brown) of the Amaranthaceae weed Chenopodium album . Freshly harvested black and brown seeds differed in their dormancy and germination responses to ambient temperature. The black seed morph of seedlot #1 was dormant and 2/3 rd of the seed population had non-deep physiological dormancy which was released by after-ripening (AR) or gibberellin (GA) treatment. The deeper dormancy of the remaining 1/3 rd non-germinating seeds required in addition ethylene and nitrate for its release. The black seeds of seedlot #2 and the brown seed morphs of both seedlots were non-dormant with 2/3 rd of the seeds germinating in the fresh mature state. The dimorphic seeds and seedlots differed in testa (outer seed coat) thickness in that thick testas of black seeds of seedlot #1 conferred coat-imposed dormancy. The dimorphic seeds and seedlots differed in their abscisic acid (ABA) and GA contents in the dry state and during imbibition in that GA biosynthesis was highest in brown seeds and ABA degradation was faster in seedlot #2. Chenopodium genes for GA and ABA metabolism were identified and their distinct transcript expression patterns were quantified in dry and imbibed C. album seeds. Phylogenetic analyses of the Amaranthaceae sequences revealed a high proportion of expanded gene families within the Chenopodium genus. The identified hormonal, molecular and morphological mechanisms and dormancy variation of the dimorphic seeds of C. album and other Amaranthaceae are compared and discussed as adaptations to variable and stressful environments.
Design and implementation of plasmonic resonators with sub-radiant and Fano modes (2009)

Design principles and implementations of plasmonic nanocavities sustaining sub-radiant and Fano-type modes are described. These structures show high sensing figures of merit and could form a basis for nanoscale optical sensors and metamaterials.
Genetic Determinants of Antibody Levels in Cerebrospinal Fluid in Multiple Sclerosis: Possible Links to Endogenous Retroviruses (2018)

The pathogenesis of multiple sclerosis (MS) has not been clarified. In addition to environmental factors; genetic determinants have been implicated in the pathogenesis of MS. Furthermore, endogenous retroviruses (ERV) might play a role in MS. The presence of oligoclonal immunoglobulin in cerebrospinal fluid (CSF) is a typical feature of MS. Recently, genetic polymorphisms in loci on human chromosomes 6, 14 and 18 have been identified as major determinants of CSF antibody levels in MS. The functional relevance of these single nucleotide polymorphisms (SNPs) remains unclear and none of them is located in an open reading frame. In previous studies, we identified ERV sequences in the vicinity of MS associated SNPs. Here, we describe the identification of ERV sequences in the neighborhood of SNPs associated with CSF antibody levels. All of the identified SNPs are located in the vicinity of ERV sequences. One of these sequences has very high homology to a sequence derived from the so-called MS-associated retrovirus (MSRV). Another cluster of three ERV sequences from the immunoglobulin heavy chain locus has retained the typical organization of retroviral genomes. These observations might shed new light on a possible association between ERVs and MS pathogenesis.
F2 screen, inheritance and cross‐resistance of field‐derived Vip3A resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) collected from Louisiana, USA (2017)

These findings provide valuable information for characterizing Vip3A resistance, resistance monitoring, and developing effective resistance management strategies for the sustainable use of the Vip3A technology. © 2017 Society of Chemical Industry.
An adaptive approach to indexing pervasive data (2001)

In a pervasive computing world data will be scattered among millions of devices and finding the right data will be a fundamental problem. Several proposed service discovery architectures can assist applications searching for data within local boundaries but there is currently no support for global access to data. We introduce an application-level protocol VIA* for building self-organizing, distributed, hierarchical data indices that adapt to dynamic query workloads. These indices efficiently route queries to relevant devices and reduce the overall workload of the system. Adapting to the query workload, VIA* uses a “query impedance” metric to approximate the optimal hierarchy for processing the expected query workload. Distributed, “logical” nodes in the interior of the hierarchy collect information about query impedance and forward this information to “data carrying” leaf nodes that react to improve the topology of the hierarchy. We present some findings from our workload testbed that demonstrate the performance and scalability characteristics of our approach and outline our research agenda
ChemInform Abstract: A Practical Synthesis of the Chinese “Nootropic” Agent Huperzine A: A Possible Lead in the Treatment of Alzheimer′s Disease. (1989)

Abstract The preparation of the title compound (XIX) according to the scheme represents the first total synthesis of this alkaloid.
Human osteoblast cells: Isolation, characterization, and growth on polymers for musculoskeletal tissue engineering (2005)

We performed a detailed examination of the isolation, characterization, and growth of human osteoblast cells derived from trabecular bone. We further examined the morphology, phenotypic gene expression, mineralization,and growth of these human osteoblasts on polyester polymers used for musculoskeletal tissue engineering. Polylactic-co-glycolic acid [PLAGA (85:15, 50:50, 75:25)], and poly-lactic acid (L-PLA, D,L-PLA) were examined. The osteoblastic expression of key phenotypic markers osteocalcin, alkaline phosphatase, collagen, and bone sialoprotein at 4 and 8 weeks was examined. Reverse transcription-polymerase chain reaction studies revealed that trabecular-derived osteoblasts were positive for all markers evaluated with higher levels expressed over long-term culture. These cells also revealed mineralization and maturation as evidenced by energy dispersive X-ray analysis and scanning electron microscopy. Growth studies on PLAGA at 50:50,75:25, and 85:15 ratios and PLA in the L and DL isoforms revealed that human osteoblasts actively grew, with significantly higher cell numbers attached to scaffolds composed of PLAGA 50:50 in the short term and PLAGA 85:15 in the long term compared with PLA (p < 0.05). We believe human cell adhesion among these polymeric materials may be dependent on differences in cellular integrin expression and extracellular matrix protein elaboration.
STEM for What? Considering Curriculum Goals for STEM (2019)

As the STEM movement gathers public and scholarly attention it is important to scrutinize its curriculum goals. Technology and education has had an uncritically positive association, and the ethical dimension of design decision making has been conspicuously absent. The goals of this theoretical paper are to develop a curriculum justification for the privileging of one form of knowledge over another. This is done by considering the natures of Science, and Technology, as interested in the natural and the artificial worlds respectively. Such considerations buy us the conclusions that context dependency of truth claims may be used as a basis for its discrimination, and that appreciating sites of contentious knowledge opens up possibilities for achieving liberatory goals for education.
Engraftment of human myelodysplastic syndrome derived cell line in transgenic severe combined immunodeficient (TG‐SCID) mice expressing human GM–CSF and IL‐3 (1998)

A transgenic SCID (TG-SCID) mouse expressing the human cytokines interleukin-3 (IL-3) and granulocyte-macrophage colony-stimulating factor (GM-CSF) has been generated with the aim of making a model system allowing the in vivo proliferation of human hematopoietic cells. Using TG-SCID mice expressing high levels (30-35 ng/ml in the serum) of human GM-CSF and IL-3, we attempted to engraft a human myeloid leukemia cell line, F-36P, derived from a myelodysplastic syndrome (MDS) patient. When F-36P cells were transferred intravenously into sublethally irradiated TG-SCID mice, extensive proliferation of F-36P cells was found 4-6 wk later. Successful engraftment, however, required the preadministration of a monoclonal antibody to mouse interleukin-2 receptor (IL-2R) beta chain, neutralizing NK activity. Surprisingly, all the transplanted TG-SCID mice engrafted with F-36P cells developed hind leg paralysis approximately 6 wk after transfer. Histological analysis demonstrated extensive invasion and formation of osteolytic lesions by the F-36P cells in the vertebrae. These data indicate that transgenic SCID mice expressing human IL-3 and GM-CSF provide a useful system for the study of human leukemia. In addition, NK cells appear to play an important role in rejection of human cells.
A modeling study of idiopathic intracranial hypertension: etiology and diagnosis (2007)

Results of the model experiments suggest that the primary cause of IIH may be a compressible, as opposed to rigid, transverse sinus, and that the observed stenosis is a necessary characteristic of the elevated pressure state.
Spectral Neugebauer-based color halftone prediction model accounting for paper fluorescence (2014)

We present a spectral model for predicting the fluorescent emission and the total reflectance of color halftones printed on optically brightened paper. By relying on extended Neugebauer models, the proposed model accounts for the attenuation by the ink halftones of both the incident exciting light in the UV wavelength range and the emerging fluorescent emission in the visible wavelength range. The total reflectance is predicted by adding the predicted fluorescent emission relative to the incident light and the pure reflectance predicted with an ink-spreading enhanced Yule-Nielsen modified Neugebauer reflectance prediction model. The predicted fluorescent emission spectrum as a function of the amounts of cyan, magenta, and yellow inks is very accurate. It can be useful to paper and ink manufacturers who would like to study in detail the contribution of the fluorescent brighteners and the attenuation of the fluorescent emission by ink halftones.
Prognostic Significance of Promoter DNA Hypermethylation of cysteine dioxygenase 1 (CDO1) Gene in Primary Breast Cancer (2016)

Using pharmacological unmasking microarray, we identified promoter DNA methylation of cysteine dioxygenase 1 (CDO1) gene in human cancer. In this study, we assessed the clinicopathological significance of CDO1 methylation in primary breast cancer (BC) with no prior chemotherapy. The CDO1 DNA methylation was quantified by TaqMan methylation specific PCR (Q-MSP) in 7 BC cell lines and 172 primary BC patients with no prior chemotherapy. Promoter DNA of the CDO1 gene was hypermethylated in 6 BC cell lines except SK-BR3, and CDO1 gene expression was all silenced at mRNA level in the 7 BC cell lines. Quantification of CDO1 methylation was developed using Q-MSP, and assessed in primary BC. Among the clinicopathologic factors, CDO1 methylation level was not statistically significantly associated with any prognostic factors. The log-rank plot analysis elucidated that the higher methylation the tumors harbored, the poorer prognosis the patients exhibited. Using the median value of 58.0 as a cut-off one, disease specific survival in BC patients with CDO1 hypermethylation showed significantly poorer prognosis than those with hypomethylation (p = 0.004). Multivariate Cox proportional hazards model identified that CDO1 hypermethylation was prognostic factor as well as Ki-67 and hormone receptor status. The most intriguingly, CDO1 hypermethylation was of robust prognostic relevance in triple negative BC (p = 0.007). Promoter DNA methylation of CDO1 gene was robust prognostic indicator in primary BC patients with no prior chemotherapy. Prognostic relevance of the CDO1 promoter DNA methylation is worthy of being paid attention in triple negative BC cancer.
A 180 mV 81.2%-Efficient Switched-Capacitor Voltage Doubler for IoT Using Self-Biasing Deep N-Well in 16-nm CMOS FinFET (2018)

We introduce the first monolithic step-up dc–dc converter operating at deep sub-1 V (i.e., 0.18–0.4 V) that outputs significant power for Internet-of-Things with a peak power efficiency of 81.2% at 50 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$ {\mu }\text{W}$ </tex-math></inline-formula> output power for the 0.18-V input and 87.1% at 300 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$ {\mu }\text{W}$ </tex-math></inline-formula> output power for 0.4 V. It is implemented in 16-nm FinFET CMOS and uses an MOS transistor as a high-density flying capacitor for energy conversion. The capacitor is arranged in a self-biased deep N-well topology, which enhances the overall efficiency by 9.5%. An integrated time-to-digital converter verifies the dc–dc output quality.
<title>Photodynamic protein incorporated in conducting polymer and sol-gel matrices: toward smart materials for information storage and processing</title> (1994)

We report our development of biomaterials for information processing and signal transduction by incorporation of photodynamic proteins into conducting polymer and sol-gel matrices. Our aim is to develop biomaterials with high optical quality, good thermal and mechanical stability, and superior opto-electronic characteristics for applications in biosensor, signal transduction, and information processing. A novel three-dimensional optical memory system based on a light transducing protein, bacteriorhodopsin, is designed and demonstrated.
High‐Quality CsPbBr3 Perovskite Films with Modal Gain above 10 000 cm−1 at Room Temperature (2023)

Abstract Halide perovskite lasers based on CsPbBr 3 micro‐ and nanoscale crystals have demonstrated fascinating performance owing to their low‐threshold lasing at room temperature and cost‐effective fabrication. However, chemically synthesized thin films of CsPbBr 3 usually have rough polycrystalline morphology along with a large amount of crystal lattice defects and, thus, are mostly utilized for the engineering of light‐emitting devices. This obstacle prevents their usage in many photonic applications. Here, a protocol to deposit large‐grain and smooth CsPbBr 3 thin films is developed. Their high quality and large scale allow to demonstrate a maximum optical gain up to 12 900 cm −1 in the spectral range of 530–540 nm, which is a record‐high value among all previously reported halide perovskites and bulk semiconductors (e.g., GaAs, GaN, etc.) at room temperature. Moreover, femtosecond laser ablation technique is employed to create high‐quality microdisc lasers on glass from these films to obtain excellent lasing characteristics. The revealed critical roles of thickness and grain size for the CsPbBr 3 films with extremely high optical gain pave the way for development of low‐threshold lasers or ultimately small nanolasers, as well as to apply them for polaritonic logical elements and integrated photonic chips.
Search for a heavy resonance decaying into a top quark and a W boson in the lepton plus jets final state at √s=13 TeV (2022)

A search for a heavy resonance decaying into a top quark and a W boson in proton-proton collisions at √s = 13 TeV is presented. The data analyzed were recorded with the CMS detector at the LHC and correspond to an integrated luminosity of 138 fb−1. The top quark is reconstructed as a single jet and the W boson, from its decay into an electron or muon and the corresponding neutrino. A top quark tagging technique based on jet clustering with a variable distance parameter and simultaneous jet grooming is used to identify jets from the collimated top quark decay. The results are interpreted in the context of two benchmark models, where the heavy resonance is either an excited bottom quark b∗ or a vector-like quark B. A statistical combination with an earlier search by the CMS Collaboration in the all-hadronic final state is performed to place upper cross section limits on these two models. The new analysis extends the lower range of resonance mass probed from 1.4 down to 0.7 TeV. For left-handed, right-handed, and vector-like couplings, b∗ masses up to 3.0, 3.0, and 3.2 TeV are excluded at 95% confidence level, respectively. The observed upper limits represent the most stringent constraints on the b∗ model to date.
Head-to-Head Comparison of Poxvirus NYVAC and ALVAC Vectors Expressing Identical HIV-1 Clade C Immunogens in Prime-Boost Combination with Env Protein in Nonhuman Primates (2015)

The finding of a safe and effective HIV/AIDS vaccine immunogen is one of the main research priorities. Here, we generated two poxvirus-based HIV vaccine candidates (NYVAC and ALVAC vectors) expressing the same clade C HIV-1 antigens in separate vectors, and we analyzed in nonhuman primates their immunogenicity profiles. The results showed that immunization with NYVAC-C induced a trend toward higher HIV-1-specific cellular and humoral immune responses than did ALVAC-C, indicating that this new NYVAC vector could be a novel optimized HIV/AIDS vaccine candidate for human clinical trials.