gebhart/patrepeval huggingface dataset:
$L^p$-Norm Bounds for Automorphic Forms via Spectral Reciprocity (2022)

Let $g$ be a Hecke-Maass cusp form on the modular surface ${\rm SL}_2(\mathbb{Z})\backslash\mathbb{H}$, namely an $L^2$-normalised nonconstant Laplacian eigenfunction on ${\rm SL}_2(\mathbb{Z})\backslash\mathbb{H}$ that is additionally a joint eigenfunction of every Hecke operator. We prove the $L^4$-norm bound $\|g\|_4\ll_{\varepsilon}λ_g^{3/304+\varepsilon}$, where $λ_g$ denotes the Laplacian eigenvalue of $g$, which improves upon Sogge's $L^4$-norm bound $\|g\|_4\llλ_g^{1/16}$ for Laplacian eigenfunctions on a compact Riemann surface by more than a six-fold power-saving. Via interpolation, this yields $L^p$-norm bounds for Hecke-Maass cusp forms that are power-saving improvements on Sogge's bounds for all $p&gt;2$. Our paper marks the first improvement of Sogge's result on the modular surface. Furthermore, these methods yield for compact arithmetic surfaces the best $L^4$-norm bound to date. Via the Watson-Ichino triple product formula, bounds for the $L^4$-norm of $g$ are reduced to bounds for certain mixed moments of $L$-functions. We bound these using two forms of spectral reciprocity. The first is a form of ${\rm GL}_3\times{\rm GL}_2\leftrightsquigarrow{\rm GL}_4\times{\rm GL}_1$ spectral reciprocity, which relates a ${\rm GL}_2$ moment of ${\rm GL}_3\times{\rm GL}_2$ Rankin-Selberg $L$-functions to a ${\rm GL}_1$ moment of ${\rm GL}_4\times{\rm GL}_1$ Rankin-Selberg $L$-functions; this can be seen as a cuspidal analogue of Motohashi's formula relating the fourth moment of the Riemann zeta function to the third moment of central values of Hecke $L$-functions. The second is a form of ${\rm GL}_4\times{\rm GL}_2\leftrightsquigarrow{\rm GL}_4\times{\rm GL}_2$ spectral reciprocity, which is a cuspidal analogue of a formula of Kuznetsov for the fourth moment of central values of Hecke $L$-functions.
Exploring the miRNA-mediated response to combined stresses in melon plants (2021)

Abstract Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop-productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of melon’s response to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress-combinations, most interactions were negative suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling evidences that the response to combined stresses cannot be easily predicted from the study individual stresses.
Novel Human Gene Transfer Vectors: Evaluation of Wild-Type and Recombinant Animal Adenoviruses in Human-Derived Cells (1999)

Major disadvantages of human adenovirus (hAd) vectors in gene therapy include preexisting or induced immune responses, and possible coreplication of recombinant hAd in the presence of wild-type hAds. These disadvantages may be overcome by using nonhuman, animal adenoviruses (aAds). We evaluated four different aAds for their potential use as viral vectors. The canine adenovirus type 2 (CAV2) and bovine adenovirus type 3 (BAV3) appeared to be suitable systems, as they infect human cells. CAV2, but not BAV3, caused cytotoxicity, and only limited (CAV2) or no (BAV3) production of infectious virus particles was observed after infection of human cell lines. CAV2 showed higher expression of endogenous genes than did BAV3 in the tested human cells. No interference between hAd and CAV2 or BAV3, such as recombination of DNA or cross-activation of virus replication, was observed in up to five passages in double-infected human cells. Transfection of cloned genomic CAV2 or BAV3 DNA into appropriate permissive cell lines rescued infectious virus. Furthermore, we produced a recombinant E1-deleted BAV3, and showed that it could infect and express a reporter gene in various human cell types. The goal was to construct and evaluate recombinant (E1-deleted) animal adenoviruses (aAds) as new vector systems for human gene therapy. The rationale for developing aAds for human use is the potential higher safety and efficiency, as compared with human adenoviruses (hAds). Coreplication and recombination with preexisting hAds should not be possible owing to lack of homology, and preexisting immunity in the general population should be limited. Of the four aAds we evaluated, BAV3 appeared to be the best candidate. It infects human cells without showing growth or cytotoxic effects, viral gene expression was barely detectable, and no trans-activation of either virus was detected in coinfections with hAd5. Rescue of virus in permissive cells, from plasmids containing the CAV2 or BAV3 genome, confirmed our approach. Furthermore, an E1-deleted recombinant BAV3 was constructed and shown to transduce and express the lacZ reporter gene in human cells.
VHL-gene Deletion in Single Renal Tubular Epithelial Cells and Renal Tubular Cysts: Further Evidence for a Cyst-dependent Progression Pathway of Clear Cell Renal Carcinoma in von Hippel-Lindau Disease (2010)

Inheritance of a mutant allele of the von Hippel-Lindau tumor suppressor gene predisposes affected individuals to develop renal cysts and clear cell renal cell carcinoma. Von Hippel-Lindau gene inactivation in single renal tubular cells has indirectly been showed by immunohistochemical staining for the hypoxia-inducible factor alpha target gene product carbonic anhydrase IX. In this study we were able to show von Hippel-Lindau gene deletion in carbonic anhydrase IX positive nonneoplastic renal tubular cells, in epithelial cells lining renal cysts and in a clear cell renal cell carcinoma of a von Hippel-Lindau patient. This was carried out by means of laser confocal microscopy and immunohistochemistry in combination with fluorescence in situ hybridization. Carbonic anhydrase IX negative normal renal tubular cells carried no von Hippel-Lindau gene deletion. Furthermore, recent studies have indicated that the von Hippel-Lindau gene product is necessary for the maintenance of primary cilia stability in renal epithelial cells and that disruption of the cilia structure by von Hippel-Lindau gene inactivation induces renal cyst formation. In our study, we show a significant shortening of primary cilia in epithelial cells lining renal cysts, whereas, single tubular cells with a von Hippel-Lindau gene deletion display to a far lesser extent signs of cilia shortening. Our in vivo results support a model in which renal cysts represent precursor lesions for clear cell renal cell carcinoma and arise from single renal tubular epithelial cells owing to von Hippel-Lindau gene deletion.
A local density-based simultaneous two-level algorithm for topographic clustering (2008)

Determining the optimum number of clusters is an ill posed problem for which there is no simple way of knowing that number without a priori knowledge. The purpose of this paper is to provide a simultaneous two-level clustering algorithm based on self organizing map, called DS2L-SOM, which learn at the same time the structure of the data and its segmentation. The algorithm is based both on distance and density measures in order to accomplish a topographic clustering. An important feature of the algorithm is that the cluster number is discovered automatically. A great advantage of the proposed algorithm, compared to the common partitional clustering methods, is that it is not restricted to convex clusters but can recognize arbitrarily shaped clusters and touching clusters. The validity and the stability of this algorithm are superior to standard two-level clustering methods such as SOM+K-means and SOM+hierarchical agglomerative clustering. This is demonstrated on a set of critical clustering problems.
Mammalian lipin phosphatidic acid phosphatases in lipid synthesis and beyond: metabolic and inflammatory disorders (2019)

The regulation of cellular lipid storage and membrane lipid composition plays a critical role in metabolic homeostasis, and dysregulation may contribute to disorders such as obesity, fatty liver, type 2 diabetes, and cardiovascular disease. The mammalian lipin proteins (lipin 1, lipin 2, and lipin 3) are phosphatidic acid phosphatase (PAP) enzymes that modulate levels of cellular triacylglycerols and phospholipids, and also regulate lipid intermediates in cellular signaling pathways. Lipin proteins also have the ability to coactivate/corepress transcription. In humans and mice, lipin gene mutations cause severe metabolic phenotypes including rhabdomyolysis (lipin 1), autoinflammatory disease (lipin 2), and impaired intestinal lipoprotein assembly (lipin 2/lipin 3). Characterization of these diseases has revealed roles for lipin PAP activity in fundamental cellular processes such as autophagy, inflammasome activation, and lipoprotein assembly. Lipin protein activity is regulated at pre- and posttranscriptional levels, which suggests a need for their ordered response to specific physiological stimuli. Challenges for the future include better elucidation of the unique biochemical and physiological properties of individual lipin family members and determination of lipin protein structure-function relationships. Further research may propel exploration of lipin proteins as viable therapeutic targets in metabolic or inflammatory disorders.
Final Progress Report: FRACTURE AND SUBCRITICAL DEBONDING IN THIN LAYERED STRUCTURES: EXPERIMENTS AND MULTI-SCALE MODELING (2005)

Final technical report detailing unique experimental and multi-scale computational modeling capabilities developed to study fracture and subcritical cracking in thin-film structures. Our program to date at Stanford has studied the mechanisms of fracture and fatigue crack-growth in structural ceramics at high temperature, bulk and thin-film glasses in selected moist environments where we demonstrated the presence of a true mechanical fatigue effect in some glass compositions. We also reported on the effects of complex environments and fatigue loading on subcritical cracking that effects the reliability of MEMS and other micro-devices using novel micro-machined silicon specimens and nanomaterial layers.
Evidence supporting the existence of a NUPR1-like family of helix-loop-helix chromatin proteins related to, yet distinct from, AT hook-containing HMG proteins (2014)

NUPR1, a small chromatin protein, plays a critical role in cancer development, progression, and resistance to therapy. Here, using a combination of structural bioinformatics and molecular modeling methods, we report several novel findings that enhance our understanding of the biochemical function of this protein. We find that NUPR1 has been conserved throughout evolution, and over time it has undergone duplications and transpositions to form other transcriptional regulators. Using threading, homology-based molecular modeling, molecular mechanics calculations, and molecular dynamics simulations, we generated structural models for four of these proteins: NUPR1a, NUPR1b, NUPR2, and the NUPR-like domain of GTF2-I. Comparative analyses of these models combined with extensive linear motif identification reveal that these four proteins, though similar in their propensities for folding, differ in size, surface changes, and sites amenable for posttranslational modification. Lastly, taking NUPR1a as the paradigm for this family, we built models of a NUPR-DNA complex. Additional structural comparisons revealed that NUPR1 defines a new family of small-groove-binding proteins that share structural features with, yet are distinct from, helix-loop-helix AT-hook-containing HMG proteins. These models and inferences should lead to a better understanding of the function of this group of chromatin proteins, which play a critical role in the development of human malignant diseases.
Indoor detection and tracking of human targets with UWB radar sensor networks (2016)

In this paper, the whole signal processing chain for an ultra-wideband (UWB) radar sensor network (RSN) is presented, starting from real measurements collected by sensor devices, and ending with the estimation of the target trajectory. The RSN is composed by one transmitter and six receivers, and monitors an indoor area of about 70 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> performing tracking of a human target. The proposed processing chain consists of: clutter removal, a novel detection scheme, one-dimensional clustering, trilateration, two-dimensional clustering, particle-based probability hypothesis density filter tracking, and data association. Numerical results show the remarkable performance of the system, resulting in a root mean square localization error of 36 cm, a value smaller than the target size. The presented experimental study show that it is possible to accurately track human targets using a UWB RSN in a densely cluttered environment.
Three‐dimensional structure of a barnase‐3'GMP complex at 2.2Å resolution (1993)

Barnase has been co-crystallized at neutral pH with its natural product the 3'-guanylic acid. The X-ray structure was solved by molecular replacement methods and refined to a final R-factor of 18.7%. The protein folding is essentially the same as that of the native form. The base recognition site is almost identical to that of the homologous binase-3'GMP complex, but the nucleotide is bound in a productive binding mode for a substrate with a syn glycosyl torsion angle allowing the general base Glu73 to hydrogen bond with the 2'O of the nucleotide as is assumed in the classical catalytic mechanism. The two molecules of the asymmetric unit form a dimer and the positions of the two nucleotides partially mimic the interaction of the RNA with the enzyme, one of the inhibitors being located in a secondary subsite.
Carbon Nanomaterials: Nitrogen Dopants in Carbon Nanomaterials: Defects or a New Opportunity? (Small Methods 1‐2/2017) (2017)

Heteroatom doping into carbon nanomaterials, including carbon nanotubes, graphene, and graphene nanoribbons is discussed by Sang Ouk Kim and co-workers in article number 1600014. Nitrogen doping provides new opportunities, including the ability to engineer various physiochemical properties of carbon nanomaterials in a stable manner with different dopant configurations. Pivotal concepts and the next steps in the field are considered.
California arbovirus (La Crosse) infections. I. Clinical and laboratory findings in 66 children with meningoencephalitis. (1973)

California encephalitis (CE) has been a significant cause of morbidity in Minnesota, accounting for 6.4% of all laboratory-documented cases of meningoencephalitis during the summers of 1967 through 1972. CE occurred in 66 children aged 6 months to 17 years. All patients were from rural or suburban areas. A mild and a severe clinical form of CE were defined with the severe form becoming more prevalent during the last two years. Focal neurologic findings were present in 16% of patients and localized abnormalities were seen in 40% of EEGs and brain scans. All patients survived but 15% had sequelae. Comparative neutralization and immunodlifusion tests indicated that La Crosse was the subtype responsible for CE in all patients appropriately studied. Since the diagnosis of CE depends on serology, antibody responses in patients during the acute illness and for two years thereafter are described. The clinical features of CE are contrasted with those of herpesvirus, mumps, and enteroviral meningoencephalitis.
Abstract A1-35: RRx-001, a novel first in class epigenetic modulator, “episensitizes” colorectal patients to FOLFIRI: Preliminary resensitization data from the Phase 2 “ROCKET” study (2015)

Abstract Background: RRx-001 is a novel systemically non-toxic pan-epigenetic modulator of DNA methyltransferases, Histone Deacetylases, and lysine demethylases with broad activity both preclinically and clinically. In the first-in-man Phase I trial, five patients who progressed on RRx-001 treatment were resensitized to previously failed therapy, warranting further investigation. Accordingly, a randomized multi-center phase II trial of RRx-001 versus regorafenib (ROCKET) has been initiated to explore the resensitization or ‘episensitization’ potential in irinotecan refractory tumors and its impact on the primary objective of overall survival. Methods: Eligible patients histological or cytological documentation of adenocarcinoma of the colon or rectum and had previously received at least oxaliplatin-, and irinotecan-based regimens with or without bevacizumab, cetuximab or panitumumab and are refractory to irinotecan. As well as ECOG 0 or 1, adequate bone marrow and hematological functions were required. In this open-label study, patients were randomized to either RRx-001 or regorafenib (2:1). RRx-001 was administered IV weekly at 16.5 mg/m2. At progression on either RRx-001 or regorafenib, patients moved to the second phase of the study and were treated with irinotecan-based therapies to investigate resensitization. Results: The study is ongoing, and, therefore, the data is preliminary; however of the four patients progressing to the second phase of the study, all have demonstrated marked decreases in CEA when treated with irinotecan post RRx-001, indicative of resensitization. CT scans, where available, confirmed CEA data. Conclusions: Preliminary results in the ROCKET study suggest resensitization of patients to previously failed therapies. Due to its broad-spectrum inhibition of epigenetic enzymes, exploration of episensitization to conventional first or second-line chemotherapy is also planned in various Phase II cancer indications in addition to CRC such as NSCLC, small cell lung cancer, sarcomas, bladder cancer and multiple myeloma. Since RRx-001 lacks any systemic toxicity, it may offer a promising alternative to currently approved hypomethylating and HDAC agents. Citation Format: Tony Reid, Jennifer Carney, Keola Beale, Chan Clayton, Huy Nguyen, Cheryl Cho-Phan, Meaghan Stirn, Shoucheng Ning, Susan Knox, Bryan Oronsky, Jan Scicinski, Scott Caroen, Christopher Parker, Gary R. Fanger, George Fisher. RRx-001, a novel first in class epigenetic modulator, “episensitizes” colorectal patients to FOLFIRI: Preliminary resensitization data from the Phase 2 “ROCKET” study. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-35.
Molecular characterisation of RecQ homologues in Arabidopsis thaliana (2000)

Members of the RecQ family of DNA helicases are involved in processes linked to DNA replication, DNA recombination and gene silencing. RecQ homologues of various animals have been described recently. Here, for the first time for plants, we characterised cDNAs of all in all six different RecQ-like proteins that are expressed to different extents in Arabidopsis thaliana. Surprisingly, three of these proteins are small in size [AtRecQl1, AtRecQl2, AtRecQl3-606, 705 and 713 amino acids (aa), respectively], whereas the two bigger proteins result from a duplication event during plant evolution [AtRecQl4A and AtRecQl4B-1150 and 1182 aa, respectively]. Another homologue (AtRecQsim, 858 aa) most probably arose by insertion of an unrelated sequence within its helicase domain. The presence of these homologues demonstrates the conservation of RecQ family functions in higher eukaryotes. We also detected a small gene (AtWRNexo) encoding 285 aa which, being devoid of any RecQ-like helicase domain, reveals a striking homology to the exonuclease domain of human Werner protein, a prominent RecQ helicase of larger size. By means of the two-hybrid assay we were able to detect an interaction between AtWRNexo and AtRecQl2, indicating that activities that reside in a single protein chain in mammals might in plants be complemented in trans.
Discovery of Novel Biomarker Candidates for Liver Fibrosis in Hepatitis C Patients: A Preliminary Study (2012)

This study identifies 20 novel fibrosis biomarker candidates. The proteins identified may help to assess hepatic fibrosis and eliminate the need for invasive liver biopsies.
Problems (1989)

Daniel Ullman, Vaclav Konecny, Jany C. Binz, M. S. Klamkin, A. Liu, K. R. S. Sastry, David M. Bloom, David Callan, C. S. Gardner, Con Amore Problem Group, Leroy F. Meyers, Donald F. Bailey, Yan-loi Wong, Edward T. H. Wang, Barry Brunson, David Graves, N. J. Lord, Y. H. Kwong, James C. Hickman, William F. Trench, Mihaly Bencze, William Watkins, Problems, Mathematics Magazine, Vol. 62, No. 1 (Feb., 1989), pp. 58-66
Voltage dependence of beta-adrenergic modulation of conduction in the canine Purkinje fiber. (1994)

Although recent voltage-clamp and microelectrode studies have demonstrated beta-adrenergic modulation of Na+ current (INa) the modulation of conduction by catecholamines and the voltage dependence of that process have not been elucidated. To determine whether voltage-dependent modulation of conduction occurs in the presence of a beta-adrenergic agonist, the effect of 1 mumol/L isoproterenol on impulse propagation in canine Purkinje fibers was examined by using a dual-microelectrode technique. At physiological membrane potentials ([K+]o 5.4 mmol/L), isoproterenol increased squared conduction velocity [theta 2, 0.39 +/- 0.25 (m/s)2 (mean +/- SD)] from 3.46 +/- 0.86 to 3.85 +/- 0.98 (m/s)2 (P &lt; .011), an 11% change, without altering the maximum first derivative of the upslope of phase 0 of the action potential (Vmax, 641 +/- 50 versus 657 +/- 47 V/s, P = NS). At transmembrane potential of -65 mV, produced by 12 mmol/L [K+]o titration, theta 2 declined 79% to 0.73 +/- 0.44 (m/s)2 as Vmax decreased 85% to 95 +/- 43 V/s (P &lt; .02). The addition of isoproterenol further decreased theta 2 to 0.49 +/- 0.33 (m/s)2 (P = .02) in parallel with a further decline in Vmax to 51 +/- 25 V/s (P &lt; .05). Isoproterenol produced a 3-mV hyperpolarizing shift of apparent Na+ channel availability curves generated from both theta 2 and Vmax, used as indexes of the fast inward INa, without changing the slopes of the relation. The relation between normalized theta 2 and Vmax over a range of depolarized potentials was linear and was not appreciably altered by isoproterenol.(ABSTRACT TRUNCATED AT 250 WORDS)
Session 2: UM Multidisciplinary Research Session: Working Across the Biological and Physical Sciences (2013)

John R. Hetling is from the Department of Bioengineering at the University of Illinois at Chicago.
High-temperature X-ray diffraction study of phase transformations in nitrogen-bearing steels (2006)

The phase composition, lattice parameters, and residual stresses in the α and γ phases of steels containing 0.14–1.2 wt % N are determined by high-temperature X-ray diffraction at 20–1200°C. A procedure is proposed for the in situ quantitative study of the Cr2N nitride dissolution kinetics and austenite grain growth when diffraction patterns are taken at high temperatures. The temperature boundaries of the decomposition of the α and γ phases and the temperature of complete dissolution of nitride phases are found. The formation of interphase residual stresses during thermal treatment is considered.
Un nouveau réseau d'interconnexion adapté aux calculateurs SIMD (1984)

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