gebhart/patrepeval huggingface dataset:
A Novel Unsaturated β-Glucuronyl Hydrolase Involved in Ulvan Degradation Unveils the Versatility of Stereochemistry Requirements in Family GH105 (2014)

Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.
Experimental investigation of acousto-optic communications (2003)

Abstract-Covert communications between underwater and aerial platforms would increase the flexibility of surface and air vehicles engaged in undersea warfare by providing a new netcentric warfare communication capability and could have a variety of commercial and oceanographic applications. Research into an acousto-optic sensor shows promise as a means for detecting acoustic data projected towards the water surface from a submerged platform. The laser-based sensor probes the water surface to detect interface vibrations caused by an impinging acoustic pressure field. A number of experimental and simulation studies were conducted to demonstrate acousto-optic sensor feasibility for obtaining robust recordings of acoustic communication signals across the air-water interface. The recorded surface velocity signals were transferred to an acoustic communication receiver that employs conventional acoustic telemetry algorithms such as adaptive equalization and Viterbi convolutional decoding to decode the signal. The detected, equalized, and decoded bit error rate performance is presented for hydrostatic, more realistic hydrodynamic water surface conditions, and hydrodynamic surface conditions while employing a surface normal tracking unit that is designed to mitigate degradation in communication performance as a result of optical signal dropout.
Constitutive Activation of AKT Contributes to the Pathogenesis and Survival of Blastoid Variants of Mantle Cell Lymphoma. (2005)

Abstract The serine/threonine protein kinase AKT [protein kinase B (PKB)] plays a pivotal role in the tumorigenesis of many human malignancies, including hematopoietic neoplasms. AKT mediates cancer cell survival and cell growth through the phosphorylation of key regulatory proteins such as FRKHL-1, MDM2 and p27. We wished to determine whether the AKT signaling pathway might be involved in the pathogenesis of mantle cell lymphoma (MCL).The activated form of AKT (pAKT) and phosphorylation of several AKT targets, including FRKHL-1, MDM2 and p27 as well as the upstream modulators PTEN and TCL-1 were analyzed by immunoblotting in 31 MCL cases (16 classic MCL and 15 MCL of the blastoid variant) and in four MCL cell lines (Granta 519, NCEB, REC-1 and Z138). PI3KCA mutation analysis at two hotspot regions (Exons 9 and 20) were completed for all cases and cell lines. Subsequently, inhibition of the PIK3/AKT-pathway with LY294002, Wortmannin and AKT-inhibitor was performed in the four cell lines. pAKT was expressed in all 15 blastoid variants of MCL and in the 4 cell lines, with high expression in 13/15 cases and low expression in 2/15 cases. In contrast, only 2/16 typical MCL expressed pAKT, at low levels. Furthermore, pAKT expression in the blastoid variants and cell lines was accompanied by the phosphorylation of multiple downstream targets of activated AKT, including the cell cycle regulatory proteins p27, FRKHL-1, MDM-2 and the apoptosis associated protein bad. 42% of the blastoid MCL cases showed loss of PTEN, while only 2 (12%) of the typical cases showed diminished PTEN expression.TCL-1 expression levels were not correlated with AKT activation and no mutations of PI3KCA were detected. Functional studies of all four MCL lines demonstrated that the phosphorylation of the downstream effectors were regulated by activated AKT:Inhibition of the PI3K/AKT pathway by both 20 μM LY294002 and 8 μM Wortmannin or 40 μM AKT-inhibitor abrogated the phosphorylation of AKT, p27, FRKHL-1, bad and MDM2 after 24 to 48 hours of treatment, and resulted in G1 arrest after 24 hours of treatment and measurable apoptosis by 48 hours. We conclude that constitutive activation of AKT contributes to the pathogenesis of the blastoid variants of MCL. One possible mechanism of AKT activation is the loss of PTEN expression. The inhibition of the PIK3/AKT pathway in MCL cell lines leads to induction of cell cycle arrest and apoptosis, raising the possibility that PI3K/AKT inhibitors may be effective in the treatment of aggressive (blastoid) variants of MCLs.
Compound Semiconductors for Terahertz Photonics (2007)

Terahertz photonics is a rapidly growing field. The ultra-fast dynamics of charge carriers in semiconductors is closely linked to the performance of THz photonic devices. We study a range of ion-implanted and nano-scale semiconductors for application in novel terahertz devices.
Relationship of normal-weight central obesity with the risk for heart failure and atrial fibrillation: analysis of a nationwide health check-up and claims database (2022)

Our analysis of a nationwide health check-up and administrative claims database including ∼1.7 million participants without prevalent CVD history demonstrated the potential impact of NWCO on the risk for HF and AF, suggesting the importance of abdominal obesity in the developing HF and AF even in normal-weight individuals.
Water exchange rates of water-soluble manganese(iii) porphyrins of therapeutical potential (2010)

The activation parameters and the rate constants of the water-exchange reactions of Mn(III)TE-2-PyP(5+) (meso-tetrakis(N-ethylpyridinium-2-yl)porphyrin) as cationic, Mn(III)TnHex-2-PyP(5+) (meso-tetrakis(N-n-hexylpyridinium-2-yl)porphyrin) as sterically shielded cationic, and Mn(III)TSPP(3-) (meso-tetrakis(4-sulfonatophenyl)porphyrin) as anionic manganese(iii) porphyrins were determined from the temperature dependence of (17)O NMR relaxation rates. The rate constants at 298 K were obtained as 4.12 x 10(6) s(-1), 5.73 x 10(6) s(-1), and 2.74 x 10(7) s(-1), respectively. On the basis of the determined entropies of activation, an interchange-dissociative mechanism (I(d)) was proposed for the cationic complexes (DeltaS(double dagger) = approximately 0 J mol(-1) K(-1)) whereas a limiting dissociative mechanism (D) was proposed for Mn(III)TSPP(3-) complex (DeltaS(double dagger) = +79 J mol(-1) K(-1)). The obtained water exchange rate of Mn(III)TSPP(3-) corresponded well to the previously assumed value used by Koenig et al. (S. H. Koenig, R. D. Brown and M. Spiller, Magn. Reson. Med., 1987, 4, 52-260) to simulate the (1)H NMRD curves, therefore the measured value supports the theory developed for explaining the anomalous relaxivity of Mn(III)TSPP(3-) complex. A magnitude of the obtained water-exchange rate constants further confirms the suggested inner sphere electron transfer mechanism for the reactions of the two positively charged Mn(iii) porphyrins with the various biologically important oxygen and nitrogen reactive species. Due to the high biological and clinical relevance of the reactions that occur at the metal site of the studied Mn(iii) porphyrins, the determination of water exchange rates advanced our insight into their efficacy and mechanism of action, and in turn should impact their further development for both diagnostic (imaging) and therapeutic purposes.
A Comparative Analysis of Content-based Geolocation in Blogs and Tweets (2018)

The geolocation of online information is an essential component in any geospatial application. While most of the previous work on geolocation has focused on Twitter, in this paper we quantify and compare the performance of text-based geolocation methods on social media data drawn from both Blogger and Twitter. We introduce a novel set of location specific features that are both highly informative and easily interpretable, and show that we can achieve error rate reductions of up to 12.5% with respect to the best previously proposed geolocation features. We also show that despite posting longer text, Blogger users are significantly harder to geolocate than Twitter users. Additionally, we investigate the effect of training and testing on different media (cross-media predictions), or combining multiple social media sources (multi-media predictions). Finally, we explore the geolocability of social media in relation to three user dimensions: state, gender, and industry.
Dual Contrastive Loss and Attention for GANs (2021)

Generative Adversarial Networks (GANs) produce impressive results on unconditional image generation when powered with large-scale image datasets. Yet generated images are still easy to spot especially on datasets with high variance (e.g. bedroom, church). In this paper, we propose various improvements to further push the boundaries in image generation. Specifically, we propose a novel dual contrastive loss and show that, with this loss, discriminator learns more generalized and distinguishable representations to incentivize generation. In addition, we revisit attention and extensively experiment with different attention blocks in the generator. We find attention to be still an important module for successful image generation even though it was not used in the recent state-of-the-art models. Lastly, we study different attention architectures in the discriminator, and propose a reference attention mechanism. By combining the strengths of these remedies, we improve the compelling state-of-the-art Fréchet Inception Distance (FID) by at least 17.5% on several benchmark datasets. We obtain even more significant improvements on compositional synthetic scenes (up to 47.5% in FID). Code and models are available at https://github.com/ningyu1991/AttentionDualContrastGAN .
Morphology-Predicted Large-Scale Transition Number in Circulating Tumor Cells Identifies a Chromosomal Instability Biomarker Associated with Poor Outcome in Castration-Resistant Prostate Cancer (2020)

Chromosomal instability (CIN) increases a tumor cell's ability to acquire chromosomal alterations, a mechanism by which tumor cells evolve, adapt, and resist therapeutics. We sought to develop a biomarker of CIN in circulating tumor cells (CTC) that are more likely to reflect the genetic diversity of patient's disease than a single-site biopsy and be assessed rapidly so as to inform treatment management decisions in real time. Large-scale transitions (LST) are genomic alterations defined as chromosomal breakages that generate chromosomal gains or losses of greater than or equal to10 Mb. Here we studied the relationship between the number of LST in an individual CTC determined by direct sequencing and morphologic features of the cells. This relationship was then used to develop a computer vision algorithm that utilizes CTC image features to predict the presence of a high (9 or more) versus low (8 or fewer) LST number in a single cell. As LSTs are a primary functional component of homologous recombination deficient cellular phenotypes, the image-based algorithm was studied prospectively on 10,240 CTCs in 367 blood samples obtained from 294 patients with progressing metastatic castration-resistant prostate cancer taken prior to starting a standard-of-care approved therapy. The resultant computer vision-based biomarker of CIN in CTCs in a pretreatment sample strongly associated with poor overall survival times in patients treated with androgen receptor signaling inhibitors and taxanes. SIGNIFICANCE: A rapidly assessable biomarker of chromosomal instability in CTC is associated with poor outcomes when detected in men with progressing mCRPC.
The Helmholtz-Hodge Decomposition—A Survey (2012)

The Helmholtz-Hodge Decomposition (HHD) describes the decomposition of a flow field into its divergence-free and curl-free components. Many researchers in various communities like weather modeling, oceanology, geophysics, and computer graphics are interested in understanding the properties of flow representing physical phenomena such as incompressibility and vorticity. The HHD has proven to be an important tool in the analysis of fluids, making it one of the fundamental theorems in fluid dynamics. The recent advances in the area of flow analysis have led to the application of the HHD in a number of research communities such as flow visualization, topological analysis, imaging, and robotics. However, because the initial body of work, primarily in the physics communities, research on the topic has become fragmented with different communities working largely in isolation often repeating and sometimes contradicting each others results. Additionally, different nomenclature has evolved which further obscures the fundamental connections between fields making the transfer of knowledge difficult. This survey attempts to address these problems by collecting a comprehensive list of relevant references and examining them using a common terminology. A particular focus is the discussion of boundary conditions when computing the HHD. The goal is to promote further research in the field by creating a common repository of techniques to compute the HHD as well as a large collection of example applications in a broad range of areas.
Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse  <i>Igf2</i> (1997)

The mouse insulin-like growth factor 2 (Igf2) locus is a complex genomic region that produces multiple transcripts from alternative promoters. Expression at this locus is regulated by parental imprinting. However, despite the existence of putative imprinting control elements in the Igf2 upstream region, imprinted transcriptional repression is abolished by null mutations at the linked H19 locus. To clarify the extent to which the Igf2 upstream region contains autonomous imprinting control elements we have performed functional and comparative analyses of the region in the mouse and human. Here we report the existence of multiple, overlapping imprinted (maternally repressed) sense and antisense transcripts that are associated with a tandem repeat in the mouse Igf2 upstream region. Regions flanking the repeat exhibit tissue-specific parental allelic methylation patterns, suggesting the existence of tissue-specific control elements in the upstream region. Studies in H19 null mice indicate that both parental allelic methylation and monoallelic expression of the upstream transcripts depends on an intact H19 gene acting in cis. The homologous region in human IGF2 is structurally conserved, with the significant exception that it does not contain a tandem repeat. Our results support the proposal that tandem repeats act to target methylation to imprinted genetic loci.
Assessment of hemispheric differences in attention with functional near-infrared spectroscopy (2015)

Functional near infrared spectroscopy (fNIRS) is a noninvasive optical imaging technique which unables the measurements of the oxy-hemoglobin and deoxy-hemoglobin (metabolic) changes associated with cognitive activity. The proposed system uses fNIRS to detect neural activities arising from an auditory oddball task at preforontal cortex. In this paper data analysis of the fNIRS measurements acquired from the forehead during cognitive tasks is presented. The aim of this study was to invastigate the differences in the hemodynamic response of right and left hemisfer in 10 healthy young. Subjects pressed a button in response to the target stimulus. The fNIRS were recorded using the `oddball' paradigm in which two stimuli (target and standard) were presented in random order by headphones. Standard deviation, mean value, max value, peak to peak (p-p), area of the under the curve are calculated for each channel. One way ANOVA analysis is applied and according to the results max value (p=0,024), standard deviation (p=0,028), sum (p=0,016) and mean value (p=0,018) are significantly different in two hemisfers. Data analysis results revealed that the blood oxygenation is higher in right frontal lobe than the left.
Practical Entropy-Compressed Rank/Select Dictionary (2006)

Rank/Select dictionaries are data structures for an ordered set $S \subset \{0,1,...,n-1\}$ to compute $\rank(x,S)$ (the number of elements in $S$ which are no greater than $x$), and $\select(i,S)$ (the $i$-th smallest element in $S$), which are the fundamental components of \emph{succinct data structures} of strings, trees, graphs, etc. In those data structures, however, only asymptotic behavior has been considered and their performance for real data is not satisfactory. In this paper, we propose novel four Rank/Select dictionaries, esp, recrank, vcode and sdarray, each of which is small if the number of elements in $S$ is small, and indeed close to $nH_0(S)$ ($H_0(S) \leq 1$ is the zero-th order \textit{empirical entropy} of $S$) in practice, and its query time is superior to the previous ones. Experimental results reveal the characteristics of our data structures and also show that these data structures are superior to existing implementations in both size and query time.
Social and Psychological Influences on Computer User Frustration (Newhagen book chapter, 2002) (2005)

As computer usage has proliferated, so has user frustration. Even devoted and knowledgeable users encounter annoying delays, incomprehensible messages, incompatible files, and indecipherable menus. The frustration generated by these problems can be personally disturbing and socially disruptive. Psychological and social perspectives on frustration may clarify the relationships among variables such as personality types, cultural factors, goal attainment, workplace anger, and computer anxiety. These perspectives may also help designers, managers, and users understand the range of responses to frustration, which could lead to effective interventions such as redesign of software, improved training, better online help, user discipline, and even resetting of national research priorities.
Characterization by a monoclonal antibody and functional analysis of a subset of bovine T lymphocytes that express BoT8, a molecule analogous to human CD8. (1986)

Monoclonal antibody (mAb) IL-A17 characterizes a subset of bovine T lymphocytes. IL-A17 recognizes a 34,000-35,000 MW doublet, designated BoT8, which is expressed on the surface of approximately 20% of peripheral blood mononuclear leucocytes (PBM), a subpopulation of lymphocytes in T-dependent areas of lymph nodes and spleen, and about 70% of thymocytes. This molecule is not expressed on B lymphocytes, monocytes/macrophages or granulocytes. Double labelling of PBM showed that the BoT8+ population is distinct from the T lymphocyte subset expressing BoT4. BoT8+ lymphocytes purified with a fluorescence-activated cell sorter (FACS) proliferated poorly in response to mitogenic and alloantigenic stimulation in the absence of exogenous growth factors. IL-A17 had no inhibitory effect on proliferation of PBM to mitogens (Con A and PHA) or alloantigens and no measurable effect on the in vitro generation of cytolytic effector cells. However, in some experiments IL-A17 was found to block partially allospecific cytolytic function mediated by bulk effector cell populations when included in 51Cr-release assays. Fractionation of effector cells generated in an allogeneic mixed leucocyte culture (MLC) demonstrated that cytotoxic cells specific for class I major histocompatibility complex (MHC) antigens reside within the BoT8+ population. Based on these data, and information reported elsewhere on alloreactive bovine T-cell clones, BoT8 is considered to be analogous to CD8 in humans and equivalent molecules in other species.
Cyclometalated Iridium(III) Complexes with Deoxyribose Substituents (2013)

Fundamental study of enzymatic nucleoside transport suffers for lack of optical probes that can be tracked noninvasively. Nucleoside transporters are integral membrane glycoproteins that mediate the salvage of nucleosides and their passage across cell membranes. The substrate recognition site is the deoxyribose sugar, often with little distinction among nucleobases. Reported here are nucleoside analogues in which emissive, cyclometalated iridium(III) complexes are "clicked" to C-1 of deoxyribose in place of canonical nucleobases. The resulting complexes show visible luminescence at room temperature and 77 K with microsecond-length triplet lifetimes. A representative complex is crystallographically characterized. Transport and luminescence are demonstrated in cultured human carcinoma (KB3-1) cells.
Mask-Ed: Breaking the Barrier of Fear of Intimate Care for Nursing Students (2017)

Mask-Ed provides a platform for the educator to create realistic scenarios around intimate care that help students prepare, on many levels, for their initial clinical experiences. [J Nurs Educ. 2017;56(9):572-574.].
RFI-641, a Potent Respiratory Syncytial Virus Inhibitor (2002)

Human respiratory syncytial virus (RSV), a paramyxovirus, is a major cause of acute upper and lower respiratory tract infections in infants, young children, and adults. RFI-641 is a novel anti-RSV agent with potent in vitro and in vivo activity. RFI-641 is active against both RSV type A and B strains. The viral specificity and the large therapeutic window of RFI-641 (>100-fold) indicate that the antiviral activity of the compound is not due to adverse effects on normal cells. The potent in vitro activity of RFI-641 can be translated to efficacy in vivo: RFI-641 is efficacious when administered prophylactically by the intranasal route in mice, cotton rats, and African green monkeys. RFI-641 is also efficacious when administered therapeutically (24 h postinfection) in the monkey model. Mechanism of action studies indicate that RFI-641 blocks viral F protein-mediated fusion and cell syncytium formation.
A Randomized, Placebo-Controlled Study of SRT2104, a SIRT1 Activator, in Patients with Moderate to Severe Psoriasis (2015)

Clinicaltrials.gov NCT01154101.