gebhart/patrepeval huggingface dataset:
Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. (1994)

Members of a new inverted repeat element family, named Stowaway, have been found in close association with more than 40 monocotyledonous and dicotyledonous plant genes listed in the GenBank and EMBL nucleic acid data bases. Stowaway elements are characterized by a conserved terminal inverted repeat, small size, target site specificity (TA), and potential form stable DNA secondary structures. Some elements are located at the extreme 3' ends of sequenced cDNAs and supply polyadenylation signals to their host genes. Other elements are in the 5' upstream regions of several genes and appear to contain previously identified cis-acting regulatory domains. Although the Stowaway elements share many structural features with the recently discovered Tourist elements, the two families share no significant sequence similarity. Together, the Stowaway and Tourist families serve to define an important new class of short inverted repeat elements found in possibly all flowering plant genomes.
Radioimmunotherapy with 131-I tositumomab enhanced survival in good prognosis relapsed and high-risk diffuse large B-cell lymphoma (DLBCL) patients receiving high-dose chemotherapy and autologous stem cell transplantation (2007)

8013 Background: The 5-year overall survival (OS) for pts with relapsed chemosensitive DLBCL with standard transplantation is approximately 40–50%. We previously piloted the addition of standard outpatient radioimmunotherapy (RIT) with 131-I tositumomab to the transplant regimen for patients with relapsed chemoresistant NHL. This phase I study demonstrated a 3 yr OS of 55% in these poor prognosis patients (JCO 23: 461–467, 2005). The current study is a follow-up phase II study in good prognosis relapsed and high risk DLBCL patients using 131-I tositumomab with BEAM (BCNU, etoposide, cytarabine, and melphalan) followed by an autologous stem cell transplant. Methods: Forty patients were accrued to the study between 2000–2005. The patients had a median age of 54 yrs (26–75) and all had a diagnosis of DLBCL. The patients had a median of two prior chemotherapies before transplant and 88% had received prior Rituximab. All patients had chemotherapy sensitive disease at the time of stem cell transplant. Following stem cell collection, all patients received a stem cell preparative regimen of 75 cGy total body dose of 131-I tositumomab (dosimetric dose day -19 and therapeutic day -12) followed by a standard BEAM transplant regimen. Autologous unpurged stem cells were infused on day 0. The median time of follow-up of the survivors is 28 months (3–68). Results: Seventy eight percent of the patients had a complete remission following the transplant. The 3 year progression free survival (PFS) is 70% (95% CI - 48 - 84%) and the 3 year OS is 81% (95% CI - 61 - 91%). The entire transplant can be delivered on an outpatient basis. No increased toxicity compared to a similar cohort receiving BEAM alone could be detected. Conclusions: The addition of 131-I tositumomab to BEAM and autologous stem cell transplant for relapsed or high-risk chemosensitive DLBCL produces a 3-yr OS of 81% without excess toxicity. This compares favorably to historical controls. This regimen is currently being tested in a phase III trial in the BMT/CTN of Rituximab/BEAM vs. 131-I tositumomab/BEAM in patients with relapsed chemosensitive DLBCL. No significant financial relationships to disclose.
Signature laminar distributions of pathology in frontotemporal lobar degeneration (2022)

Frontotemporal lobar degeneration (FTLD) with either tau (FTLD-tau) or TDP-43 (FTLD-TDP) inclusions are distinct proteinopathies that frequently cause similar frontotemporal dementia (FTD) clinical syndromes. FTD syndromes often display macroscopic signatures of neurodegeneration at the level of regions and networks, but it is unclear if subregional laminar pathology display patterns unique to proteinopathy or clinical syndrome. We hypothesized that FTLD-tau and FTLD-TDP accumulate pathology in relatively distinct cortical layers independent of clinical syndrome, with greater involvement of lower layers in FTLD-tau. The current study examined 170 patients with either FTLD-tau (n = 73) or FTLD-TDP (n = 97) spanning dementia and motor phenotypes in the FTD spectrum. We digitally measured the percent area occupied by tau and TDP-43 pathology in upper layers (I-III), lower layers (IV-VI), and juxtacortical white matter (WM) from isocortical regions in both hemispheres where available. Linear mixed-effects models compared ratios of upper to lower layer pathology between FTLD groups and investigated relationships with regions, WM pathology, and global cognitive impairment while adjusting for demographics. We found lower ratios of layer pathology in FTLD-tau and higher ratios of layer pathology in FTLD-TDP, reflecting lower layer-predominant tau pathology and upper layer-predominant TDP-43 pathology, respectively (p < 0.001). FTLD-tau displayed lower ratios of layer pathology related to greater WM tau pathology (p = 0.002) and to earlier involved/severe pathology regions (p = 0.007). In contrast, FTLD-TDP displayed higher ratios of layer pathology not related to either WM pathology or regional severity. Greater cognitive impairment was associated with higher ratios of layer pathology in FTLD-tau (p = 0.018), but was not related to ratios of layer pathology in FTLD-TDP. Lower layer-predominant tau pathology and upper layer-predominant TDP-43 pathology are proteinopathy-specific, regardless of clinical syndromes or regional networks that define these syndromes. Thus, patterns of laminar change may provide a useful anatomical framework for investigating how degeneration of select cells and corresponding laminar circuits influence large-scale networks and clinical symptomology in FTLD.
Uncertain flexoffers, a scalable, uncertainty-aware model for energy flexibility (2022)

The usage of Renewable Energy Sources in electricity grids is spreading more and more, and energy flexibility has a crucial role in it. Many models for flexibility have been proposed; in particular, Flex-Offer (FO) is an approximate model with the following properties: i) it models flexibility from different device types in an unified format; ii) it is scalable with respect to optimization for long time horizons, and aggregation of many loads; iii) it captures most/all of the available flexibility. This work proposes an extension of that model, uncertain FlexOffers (UFOs), which has the same properties, plus iv) considers the uncertainty affecting flexibility over long time horizons. We show that UFOs are 5 orders of magnitude faster than exact models for optimization, can retain 88.3% of the total flexibility when imbalance penalties are high, and allow to aggregate up to 3000 loads and up to 96 time units in less than 30 minutes.
Implementation and Evaluation of Improved Gaussian Sampling for Lattice Trapdoors (2018)

We report on our implementation of a new Gaussian sampling algorithm for lattice trapdoors. Lattice trapdoors are used in a wide array of lattice-based cryptographic schemes including digital signatures, attributed-based encryption, program obfuscation and others. Our implementation provides Gaussian sampling for trapdoor lattices with prime moduli, and supports both single- and multi-threaded execution. We experimentally evaluate our implementation through its use in the GPV hash-and-sign digital signature scheme as a benchmark. We compare our design and implementation with prior work reported in the literature. The evaluation shows that our implementation 1) has smaller space requirements and faster runtime, 2) does not require multi-precision floating-point arithmetic, and 3) can be used for a broader range of cryptographic primitives than previous implementations.
Spatial organization of RNA polymerase and its relationship with transcription in <i>Escherichia coli</i> (2019)

Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in <i>Escherichia coli</i> and <i>Bacillus subtilis</i> cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in <i>E. coli</i> cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ<sup>70</sup> was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.
ChemInform Abstract: Research on Antiviral Agents. Part 5. Lithiation of 6‐Methyluracil as a New and Efficient Entry to C(6)‐Substituted Uracils. (1996)

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.
ChemInform Abstract: N<sup>6</sup>‐Substituted Adenosines, Cytokinin and Antitumor Activities. (2012)

Abstract The synthesis of a series of N 6 ‐substituted adenosines is described.
Identification of multidrug resistance protein 1 (MRP1/ABCC1) as a molecular gate for cellular export of cobalamin (2009)

Cobalamin (Cbl, vitamin B(12)) deficiency in humans is a cause of hematologic and neurologic disorders. We show here that the cellular export of Cbl, in contrast to the carrier- and receptor-dependent cellular import of Cbl, occurs by transmembrane transport of "free" Cbl. Screening of candidate transporters by cellular gene silencing showed a role in cellular Cbl efflux of the ATP-binding cassette (ABC)-drug transporter, ABCC1, alias multidrug resistance protein 1 (MRP1), which is present in the basolateral membrane of intestinal epithelium and in other cells. The ability of MRP1 to mediate ATP-dependent Cbl transport was confirmed by vesicular transport experiments, and a physiologic role of MRP1 in mammalian Cbl homeostasis is indicated by the phenotype of knockout mice with targeted disruption of MRP1. These animals have a reduced concentration of Cbl in plasma and in the storage organs liver and kidney. In contrast, Cbl accumulates in the terminal part of the intestine of these mice, suggesting a functional malabsorption because of a lower epithelial basolateral Cbl efflux. The identification of this Cbl export mechanism now allows the delineation of a coherent pathway for Cbl trafficking from food to the body cells.
weHelp: A Reference Architecture for Social Recommender Systems (2009)

Recommender systems have become increasingly popular. Most of the research on recommender systems has focused on recommendation algorithms. There has been relatively little research, however, in the area of generalized system architectures for recommendation systems. In this paper, we introduce <i>weHelp</i>: a reference architecture for social recommender systems - systems where recommendations are derived automatically from the aggregate of logged activities conducted by the system's users. Our architecture is designed to be application and domain agnostic. We feel that a good reference architecture will make designing a recommendation system easier; in particular, weHelp aims to provide a practical design template to help developers design their own well-modularized systems.
Wearable optical-digital assistive device for low vision students (2016)

People with low vision have limited residual vision that can be greatly enhanced through high levels of magnification. Current assistive technologies are tailored for far field or near field magnification but not both. In collaboration with L.V. Prasad Eye Institute (LVPEI), a wearable, optical-digital assistive device was developed to meet the near and far field magnification needs of students. The critical requirements, system architecture and design decisions for each module were analyzed and quantified. A proof-of-concept prototype was fabricated that can achieve magnification up to 8x and a battery life of up to 8 hours. Potential user evaluation with a Snellen chart showed identification of characters not previously discernible. Further feedback suggested that the system could be used as a general accessibility aid.
Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4 (2021)

Mechanisms by which noncoding genetic variation influences gene expression remain only partially understood but are considered to be major determinants of phenotypic diversity and disease risk. Here, we evaluated effects of >50 million single-nucleotide polymorphisms and short insertions/deletions provided by five inbred strains of mice on the responses of macrophages to interleukin-4 (IL-4), a cytokine that plays pleiotropic roles in immunity and tissue homeostasis. Of >600 genes induced >2-fold by IL-4 across the five strains, only 26 genes reached this threshold in all strains. By applying deep learning and motif mutation analyses to epigenetic data for macrophages from each strain, we identified the dominant combinations of lineage-determining and signal-dependent transcription factors driving IL-4 enhancer activation. These studies further revealed mechanisms by which noncoding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-differential patterns of gene expression and phenotypic diversity.
Long-term Outcome of Cochlear Implant in Patients with Chronic Otitis Media: One-stage Surgery Is Equivalent to Two-stage Surgery (2014)

This study compared long-term speech performance after cochlear implantation (CI) between surgical strategies in patients with chronic otitis media (COM). Thirty patients with available open-set sentence scores measured more than 2 yr postoperatively were included: 17 who received one-stage surgeries (One-stage group), and the other 13 underwent two-stage surgeries (Two-stage group). Preoperative inflammatory status, intraoperative procedures, postoperative outcomes were compared. Among 17 patients in One-stage group, 12 underwent CI accompanied with the eradication of inflammation; CI without eradicating inflammation was performed on 3 patients; 2 underwent CIs via the transcanal approach. Thirteen patients in Two-stage group received the complete eradication of inflammation as first-stage surgery, and CI was performed as second-stage surgery after a mean interval of 8.2 months. Additional control of inflammation was performed in 2 patients at second-stage surgery for cavity problem and cholesteatoma, respectively. There were 2 cases of electrode exposure as postoperative complication in the two-stage group; new electrode arrays were inserted and covered by local flaps. The open-set sentence scores of Two-stage group were not significantly higher than those of One-stage group at 1, 2, 3, and 5 yr postoperatively. Postoperative long-term speech performance is equivalent when either of two surgical strategies is used to treat appropriately selected candidates.
Multi-Objective Ease-Off Optimization of Hypoid Gears for Their Efficiency, Noise and Durability Performances (2011)

Micro-geometry optimization has become an important phase of gear design that can remarkably enhance gear performance. For spiral bevel and hypoid gears, micro-geometry is typically represented by ease-off topography. The optimal ease-off shape can be defined as the outcome of a process where generally conflicting objective functions are simultaneously minimized (or maximized), in the presence of constraints. This matter naturally lends itself to be framed as a multi-objective optimization problem. This paper proposes a general algorithmic framework for ease-off multi-objective optimization, with special attention to computational efficiency. Its implementation is fully detailed. A simulation model for loaded tooth contact analysis is assumed to be available. The proposed method is tested on a face-hobbed hypoid gear set. Three objectives are defined: maximization of mechanical efficiency, minimization of loaded transmission error, minimization of maximum contact pressure. Bound constraints on the design variables are imposed, as well as a nonlinear constraint aimed at keeping the loaded contact pattern inside a predefined allowable contact region. The results show that the proposed method can obtain optimal ease-off topographies that significantly improve the basic design performances. It is also evident that the method is general enough to handle geometry optimization of any gear type.
Dok-7 regulates neuromuscular synapse formation by recruiting Crk and Crk-L (2010)

Agrin, released by motor neurons, promotes neuromuscular synapse formation by stimulating MuSK, a receptor tyrosine kinase expressed in skeletal muscle. Phosphorylated MuSK recruits docking protein-7 (Dok-7), an adaptor protein that is expressed selectively in muscle. In the absence of Dok-7, neuromuscular synapses fail to form, and mutations that impair Dok-7 are a major cause of congenital myasthenia in humans. How Dok-7 stimulates synaptic differentiation is poorly understood. Once recruited to MuSK, Dok-7 directly stimulates MuSK kinase activity. This unusual activity of an adapter protein is mediated by the N-terminal region of Dok-7, whereas most mutations that cause congenital myasthenia truncate the C-terminal domain. Here, we demonstrate that Dok-7 also functions downstream from MuSK, and we identify the proteins that are recruited to the C-terminal domain of Dok-7. We show that Agrin stimulates phosphorylation of two tyrosine residues in the C-terminal domain of Dok-7, which leads to recruitment of two adapter proteins: Crk and Crk-L. Furthermore, we show that selective inactivation of Crk and Crk-L in skeletal muscle leads to severe defects in neuromuscular synapses in vivo, revealing a critical role for Crk and Crk-L downstream from Dok-7 in presynaptic and postsynaptic differentiation.
Integrated nanoplasmonic-nanofluidic biosensors with targeted delivery of analytes (2010)

Performances of the biosensors are often limited by the depletion zones created around the sensing area which impede the effective analyte transport. To overcome this limitation, we propose and demonstrate a nanoplasmonic-nanofluidic sensor enabling targeted delivery of analytes to the sensor surface with dramatic improvements in mass transport efficiency. Our sensing platform is based on extraordinary light transmission effect in suspended plasmonic nanoholes. This scheme allows three-dimensional control of the fluidic flow by connecting separate layers of microfluidic channels through plasmonic/nanofluidic holes. To implement the proposed sensor platform, we also introduce a lift-off free nanofabrication method.
Finite-difference time-domain analysis of bandgap characteristics of transversely probed hollow-core photonic crystal fibers (2010)

In this paper, bandgap characteristics of transversely probed hollow-core photonic crystal fibers (HC-PCFs) are numerically investigated by FDTD analysis. The transmission characteristic of the transverse trapping beam is described using concept of photonic partial bandgap. The field and intensity distribution are monitored at the central hollow-core for both TE and TM modes illuminated in the Γ-M direction. From the numerical results obtained, it is found that photonic stop bands are formed in the transmission spectrum. It is inferred that such partial bandgap studies are important for the application of HC-PCFs in the well-known area of optical tweezers where an efficient trapping can be performed inside the hollow-core.
Bragg wavelength sensitivity of higher order modes to temperature and strain in highly birefringent microstructured fibers (2013)

Summary form only given. Single mode microstructured fibers (MSF) are a subject of extensive research for over a decade now, mainly due to the fact that by changing the topology and distribution of the air holes, the fiber guiding (therefore also sensing) properties can be significantly modified and tailored to desired purposes [1]. Furthermore we have recently reported [2] that greater polarimetric sensitivities can be achieved in higher order modes (as their mode maxima are closer to the cladding hollow regions) of appropriately designed highly birefringent (HB) MSFs.In this paper we report for the llow regions) of appropriately designed highly birefringent (HB) MSFs. first time to our knowledge the results of a success (FBG) inscription in a dual mode HB written with a KrF nanosecond excimer laser in the Talbot interferometer set-up [3 spectrum of a fabricated structure i s presented in Fig. 1a. The three dual peaks visible in the Bragg reflection of the three modes propagated in the fiber. As we used reasonably short pieces (approx. 0.5 m) of the fiber (spliced on both ends with a standard SMF-28) for FBG inscription, we have noticed not only the fundamental and second order mode, but also a third order mode (with confinement loss of approx. 15 dB/m [2]) propagating in the fiber. Furthermore the difference between the effective refractive indices of the polarization modes causes the Bragg peak split into the dual peak structure (with Bragg peak separation strongly correlated with the phase birefringence).In Fig. 1b. and 1c. we present a modes to external strain and temperature changes. The B shift is comparable for all of the propagated modes (with approx. 1.1 pm/με strain sensitivity and 10 pm/K temperature sensitivity) and similar to what was reported for standard FBGs (1.2 pm/με and 13.7 pm/K at 1550 nm [4]). An additional phenomenon in HB fiber based sensors is the birefringence change due to external perturbations (e.g. strain, temperature, etc.), which in the Bragg wavelength domain corresponds to the Bragg peak separation (ǻB=Bx-By) change. We have observed the ǻB of the second order mode (E21) of approximately 0.01 nm which is in agreement with the E21 mode polarimetric strain sensitivity of 4.94Â104 rad/εÂm reported in [2]. Therefore we show that HB MSFs with enhanced sensitivity of higher order modes can be successfully used as fiber optic sensors in the convenient FBG configurations.