gebhart/patrepeval huggingface dataset:
2,2,3-Tribromopropanal as a Versatile Reagent in the Skraup-Type Synthesis of 3-Bromoquinolin-6-ols (2014)

2,2,3-Tribromopropanal, a reagent which almost became forgotten in the chemical literature after its first application in the 1950s, is used for the one-step transformation of diversely substituted 4-nitro- and 4-methoxyanilines into 3-bromo-6-nitroquinolines and 3-bromo-6-methoxyquinolines. These intermediates are then converted, in one further step, into 3-bromoquinolin-6-ols, which may carry additional substituents at positions 7 and 8.
Postkontrastní magnetická rezonance verzus SPECT Thalliová scintigrafie v detekci viabilního myokardu. Prospektivní srovnávací studie (2006)

Ucel studie: Cilem studie bylo srovnat postkontrastni zobrazeni magnetickou rezonanci (KMR) a jednofotonovou emisni tomografii využivajici 201Thallium chloridu (SPECT Tl) v hodnoceni viability myokardu. Metodika: Do studie byli zařazeni pacienti s chronickým koronarnim onemocněnim a systolickou dysfunkci leve komory, u kterých byla planovana revaskularizace myokardu. Systolicka dysfunkce leve komory byla definovana ejekcni frakci (EF) ≤ 45 %. KMR byla provedena s využitim „Inversion Recovery Turbo FLASH (fast low-angle shot)“ sekvence. SPECT Tl zobrazeni bylo provedeno ctyři hodiny po podani radiofarmaka. Výsledky: Do studie bylo zařazeno 40 nemocných. Kontrolni vysetřeni EF po revaskularizaci bylo provedeno u 32 z nich. Souhlasne hodnoceni viability mezi oběma metodami bylo pozorovano u 1065 (78,3 %) segmentů, což odpovida pouze průměrne shodě (kappa 0,336). 96 SPECT Tl viabilnich segmentů bylo popsano jako neviabilni při KMR a 199 SPECT Tl neviabilnich segmentů splňovalo kriteria viability dle KMR. U nemocných, kteři podstoupili kontrolni vysetřeni po revaskularizaci EF stoupla o 5,5 % (z 33,6 na 39,2 %). Zavislost mezi množstvim dysfunkcni viabilni tkaně a změnou EF byla velmi slaba a statisticky nevýznamna u obou srovnavaných metod. Zavěr: Při srovnani KMR a SPECT Tl v hodnoceni viability myokardu nebyla pozorovana dobra shoda. Neprokazali jsme přinos viability urcene oběma metodami pro predikci zlepseni systolicke funkce leve komory po revaskularizaci.
Lack of the Light-Harvesting Complex CP24 Affects the Structure and Function of the Grana Membranes of Higher Plant Chloroplasts (2006)

The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C(2)S(2)M(2) light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C(2)S(2) supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.
Biodegradable electronics: cornerstone for sustainable electronics and transient applications (2016)

Electronic devices have become ubiquitous in modern society and are prevalent in every facet of human activities.
Lift forces on a cylindrical particle in plane Poiseuille flow of shear thinning fluids (2003)

Lift forces on a cylindrical particle in plane Poiseuille flow of shear thinning fluids are investigated by direct numerical simulation. Previous works on this topic for Newtonian fluids show that the two-dimensional channel can be divided into alternating regions defined by the stability of the particle’s equilibrium. We observe stability regions with the same pattern in flows of shear thinning fluids and study the effects of shear thinning properties on the distribution of the stability regions. Joseph and Ocando [J. Fluid Mech. 454, 263 (2002)] analyzed the role of the slip velocity Us=Uf−Up and the angular slip velocity Ωs=Ωp−Ωf on migration and lift in plane Poiseuille flow of Newtonian fluids. They concluded that the discrepancy Ωs−Ωse, where Ωse is the angular slip velocity at equilibrium, changes sign across the equilibrium position. In this paper we verify that this conclusion holds in shear thinning fluids. Correlations for lift forces may be constructed by analogy with the classical lift formula L=CUΓ of aerodynamics and the proper analogs of U and Γ in the present context are Us and Ωs−Ωse. Using dimensionless parameters, the correlation is a power law near the wall and a linear relation (which can be taken as a power law with the power of one) near the centerline. The correlations are compared to analytical expressions for lift forces in the literature and we believe that the correlations capture the essence of the mechanism of the lift force. Our correlations for lift forces can be made completely explicit provided that the correlations relating Us and Ωs to prescribed parameters are obtained.
Anisotropic Swirling Surface Acoustic Waves from Inverse Filtering for On-Chip Generation of Acoustic Vortices (2015)

From radio-electronics signal analysis to biological sample actuation, surface acoustic waves (SAWs) are involved in a multitude of modern devices. However, only the most simple standing or progressive waves such as plane and focused waves have been explored so far. In this paper, we expand the SAW toolbox with a wave family named "swirling surface acoustic waves" which are the 2D anisotropic analogue of bulk acoustic vortices. Similarly to their 3D counterpart, they appear as concentric structures of bright rings with a phase singularity in their center resulting in a central dark spot. After the rigorous mathematical definition of these waves, we synthesize them experimentally through the inverse filtering technique revisited for surface waves. For this purpose, we design a setup combining arrays of interdigitated transducers and a multichannel electronic that enables one to synthesize any prescribed wave field compatible with the anisotropy of the substrate in a region called the “acoustic scene.” This work opens prospects for the design of integrated acoustic vortex generators for on-chip selective acoustic tweezing.
Quantifying the uncertainty in an AVO interpretation (2002)

Abstract Lithologic interpretations of amplitude variation with offset (AVO) information are ambiguous both because different lithologies occupy overlapping ranges of elastic properties, and because angle-dependent reflection coefficients estimated from seismic data are uncertain. This paper presents a method for quantifying and combining these two components of uncertainty to get a full characterization of the uncertainty associated with an AVO-based lithologic interpretation. The result of this approach is a compilation of all the lithologies that are consistent with the observed AVO behavior, along with a probability of occurrence for each lithology. A 2-D line from the North Sea illustrates how the method might be applied in practice. For any data set, the interaction between the geologic and measurement components of uncertainty may significantly affect the overall uncertainty in a lithologic interpretation.
BiEntropy - The Approximate Entropy of a Finite Binary String (2013)

We design, implement and test a simple algorithm which computes the approximate entropy of a finite binary string of arbitrary length. The algorithm uses a weighted average of the Shannon Entropies of the string and all but the last binary derivative of the string. We successfully test the algorithm in the fields of Prime Number Theory (where we prove explicitly that the sequence of prime numbers is not periodic), Human Vision, Cryptography, Random Number Generation and Quantitative Finance.
Protein kinase D1 regulates matrix metalloproteinase expression and inhibits breast cancer cell invasion (2009)

Our results identify decreased expression of the PKD1 as a marker for invasive breast cancer. They further suggest that the loss of PKD1 expression increases the malignant potential of breast cancer cells. This may be due to the function of PKD1 as a negative regulator of MMP expression. Our data suggest re-expression of PKD1 as a potential therapeutic strategy.
Realization of Integrated Coherent LiDAR (2019)

LiDAR (Light Detection and Ranging) captures high-definition real-time 3D images of the surrounding environment through active sensing with infrared lasers. It has unique advantages that can compensate the fundamental limitations in camera-based 3D imaging via vision algorithms or RADARs, which makes it an important sensing modality to guarantee robust autonomy in self-driving cars. However, high price tag of existing commercial LiDAR modules based on mechanical beam scanners and intensity-based detection scheme makes them unusable in the context of mass produced consumer products.The focus of thesis is on the integrated coherent LiDAR with optical phased array-based solid-state beam steering, which has great potential to dramatically bring down the cost of a LiDAR module. It begins with an overview of LiDAR implementation options and system requirements in the context of autonomous vehicles, which leads us to conclude that beam-steering coherent FMCW LiDAR in optical C-band is indeed the best implementation strategy to realize low-cost automotive LiDARs. Motivated by this observation, a quantitative framework for evaluating FMCW LiDAR performance is also introduced to predict the design that satisfies car-grade performance requirements. Then the thesis presents the silicon implementation results from our single-chip optical phased array and integrated coherent LiDAR prototype. Our implementations leverage the 3D heterogeneous integration platform, where custom silicon photonics and nanoscale CMOS fabricated at a 300 mm wafer facility are combined at the wafer-scale to minimize the unit cost without I/O density issues. After discussing remaining challenges and possible ways to enhance the operating range and system reliability, this thesis finally addresses the problem of fundamental trade-off between phase noise and wavelength tuning in FMCW laser source, and present circuit- and algorithm-level techniques to enable FMCW measurements beyond inherent laser coherence range limit.
UNPU: A 50.6TOPS/W unified deep neural network accelerator with 1b-to-16b fully-variable weight bit-precision (2018)

Deep neural network (DNN) accelerators [1-3] have been proposed to accelerate deep learning algorithms from face recognition to emotion recognition in mobile or embedded environments [3]. However, most works accelerate only the convolutional layers (CLs) or fully-connected layers (FCLs), and different DNNs, such as those containing recurrent layers (RLs) (useful for emotion recognition) have not been supported in hardware. A combined CNN-RNN accelerator [1], separately optimizing the computation-dominant CLs, and memory-dominant RLs or FCLs, was reported to increase overall performance, however, the number of processing elements (PEs) for CLs and RLs was limited by their area and consequently, performance was suboptimal in scenarios requiring only CLs or only RLs. Although the PEs for RLs can be reconfigured into PEs for CLs or vice versa, only a partial reconfiguration was possible resulting in marginal performance improvement. Moreover, previous works [1-2] supported a limited set of weight bit precisions, such as either 4b or 8b or 16b. However, lower weight bit-precisions can achieve better throughput and higher energy efficiency, and the optimal bit-precision can be varied according to different accuracy/performance requirements. Therefore, a unified DNN accelerator with fully-variable weight bit-precision is required for the energy-optimal operation of DNNs within a mobile environment.
Nosocomial bloodstream infections in pediatric patients in United States hospitals: epidemiology, clinical features and susceptibilities (2003)

Nosocomial BSI occurred predominantly in very young and/or critically ill children. Gram-positive pathogens predominated across all ages, and increasing antimicrobial resistance was observed in pediatric patients.
Pseudo-Cyclization through Intramolecular Hydrogen Bond Enables Discovery of Pyridine Substituted Pyrimidines as New Mer Kinase Inhibitors (2020)

Abnormal activation or overexpression of Mer receptor tyrosine kinase has been implicated in survival signaling and chemoresistance in many human cancers. Consequently, Mer is a promising novel cancer therapeutic target. A structure-based drug design approach using a pseudo-ring replacement strategy was developed and validated to discover a new family of pyridinepyrimidine analogs as potent Mer inhibitors. Through SAR studies, 10 (UNC2250) was identified as the lead compound for further investigation based on high selectivity against other kinases and good pharmacokinetic properties. When applied to live cells, 10 inhibited steady-state phosphorylation of endogenous Mer with an IC50 of 9.8 nM and blocked ligand-stimulated activation of a chimeric EGFR-Mer protein. Treatment with 10 also resulted in decreased colony-forming potential in rhabdoid and NSCLC tumor cells, thereby demonstrating functional anti-tumor activity. The results provide a rationale for further investigation of this compound for therapeutic application in patients with cancer.
Berberine suppresses gero-conversion from cell cycle arrest to senescence (2013)

Berberine (BRB), a natural alkaloid, has a long history of medicinal use in both Ayurvedic and old Chinese medicine. Recently, available as a dietary supplement, Berberine is reported to have application in treatment of variety diseases. Previously we observed that BRB inhibited mTOR/S6 signaling concurrently with reduction of the level of endogenous oxidants and constitutive DNA damage response. We currently tested whether Berberine can affect premature, stress-induced cellular senescence caused by mitoxantrone. The depth of senescence was quantitatively measured by morphometric parameters, senescence-associated β-galactosidase, induction of p21WAF1, replication stress (γH2AX expression), and mTOR signaling; the latter revealed by ribosomal S6 protein (rpS6) phosphorylation. All these markers of senescence were distinctly diminished, in a concentration-dependent manner, by Berberine. In view of the evidence that BRB localizes in mitochondria, inhibits respiratory electron chain and activates AMPK, the observed attenuation of the replication stress-induced cellular senescence most likely is mediated by AMPK that leads to inhibition of mTOR signaling. In support of this mechanism is the observation that rhodamine123, the cationic probe targeting mitochondrial electron chain, also suppressed rpS6 phosphorylation. The present findings reveal that: (a) in cells induced to senescence BRB exhibits gero-suppressive properties by means of mTOR/S6 inhibition; (b) in parallel, BRB reduces the level of constitutive DNA damage response, previously shown to report oxidative DNA damage by endogenous ROS; (c) there appears to a causal linkage between the (a) and (b) activities; (d) the in vitro model of premature stress-induced senescence can be used to assess effectiveness of potential gero-suppressive agents targeting mTOR/S6 and ROS signaling; (e) since most of the reported beneficial effects of BRB are in age-relate diseases, it is likely that gero-suppression is the primary activity of this traditional medicine.
Semi-Supervised Learning via Regularized Boosting Working on Multiple Semi-Supervised Assumptions (2010)

Semi-supervised learning concerns the problem of learning in the presence of labeled and unlabeled data. Several boosting algorithms have been extended to semi-supervised learning with various strategies. To our knowledge, however, none of them takes all three semi-supervised assumptions, i.e., smoothness, cluster, and manifold assumptions, together into account during boosting learning. In this paper, we propose a novel cost functional consisting of the margin cost on labeled data and the regularization penalty on unlabeled data based on three fundamental semi-supervised assumptions. Thus, minimizing our proposed cost functional with a greedy yet stagewise functional optimization procedure leads to a generic boosting framework for semi-supervised learning. Extensive experiments demonstrate that our algorithm yields favorite results for benchmark and real-world classification tasks in comparison to state-of-the-art semi-supervised learning algorithms, including newly developed boosting algorithms. Finally, we discuss relevant issues and relate our algorithm to the previous work.
IP3 Receptors: Toward Understanding Their Activation (2010)

Inositol 1,4,5-trisphosphate receptors (IP(3)R) and their relatives, ryanodine receptors, are the channels that most often mediate Ca(2+) release from intracellular stores. Their regulation by Ca(2+) allows them also to propagate cytosolic Ca(2+) signals regeneratively. This brief review addresses the structural basis of IP(3)R activation by IP(3) and Ca(2+). IP(3) initiates IP(3)R activation by promoting Ca(2+) binding to a stimulatory Ca(2+)-binding site, the identity of which is unresolved. We suggest that interactions of critical phosphate groups in IP(3) with opposite sides of the clam-like IP(3)-binding core cause it to close and propagate a conformational change toward the pore via the adjacent N-terminal suppressor domain. The pore, assembled from the last pair of transmembrane domains and the intervening pore loop from each of the four IP(3)R subunits, forms a structure in which a luminal selectivity filter and a gate at the cytosolic end of the pore control cation fluxes through the IP(3)R.
Cloning and characterisation of the<i>S.pombe rad15</i>gene, a homologue to the<i>S.cerevisiae RAD3</i>and human<i>ERCC2</i>genes (1992)

The RAD3 gene of Saccharomyces cerevisiae encodes an ATP-dependent 5'-3' DNA helicase, which is involved in excision repair of ultraviolet radiation damage. By hybridisation of a Schizosaccharomyces pombe genomic library with a RAD3 gene probe we have isolated the S. pombe homologue of RAD3. We have also cloned the rad15 gene of S. pombe by complementation of radiation-sensitive phenotype of the rad15 mutant. Comparison of the restriction map and DNA sequence, shows that the S. pombe rad15 gene is identical to the gene homologous to S. cerevisiae RAD3, identified by hybridisation. The S. pombe rad15.P mutant is highly sensitive to UV radiation, but only slightly sensitive to ionising radiation, as expected for a mutant defective in excision repair. DNA sequence analysis of the rad15 gene indicates an open reading frame of 772 amino acids, and this is consistent with a transcript size of 2.6 kb as detected by Northern analysis. The predicted rad15 protein has 65% identity to RAD3 and 55% identity to the human homologue ERCC2. This homology is particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that, like the S. cerevisiae RAD3 gene, the S. pombe rad15 gene is essential for viability, suggesting that the protein product has a role in cell proliferation and not solely in DNA repair.
Affinity Maturation of an Epidermal Growth Factor Receptor Targeting Human Monoclonal Antibody ER414 by CDR Mutation (2012)

It is well established that blocking the interaction of EGFR with growth factors leads to the arrest of tumor growth, resulting in tumor cell death. ER414 is a human monoclonal antibody (mAb) derived by guided selection of the mouse mAb A13. The ER414 exhibited a ~17-fold lower affinity and, as a result, lower efficacy of inhibition of the EGF-mediated tyrosine phosphorylation of EGFR when compared with mAb A13 and cetuximab. We performed a stepwise in vitro affinity maturation to improve the affinity of ER414. We obtained a 3D model of ER414 to identify the amino acids in the CDRs that needed to be mutated. Clones were selected from the phage library with randomized amino acids in the CDRs and substitution of amino acids in the HCDR3 and LCDR1 of ER414 led to improved affinity. A clone, H3-14, with a ~20-fold increased affinity, was selected from the HCDR3 randomized library. Then three clones, ER2, ER78 and ER79, were selected from the LCDR1 randomized library based on the H3-14 but did not show further increased affinities compared to that of H3-14. Of the three, ER2 was chosen for further characterization due to its better expression than others. We successfully performed affinity maturation of ER414 and obtained antibodies with a similar affinity as cetuximab. And antibody from an affinity maturation inhibits the EGF-mediated tyrosine phosphorylation of EGFR in a manner similar to cetuximab.
Affinity Purifications of Aldose Reductase and Xylitol Dehydrogenase from the Xylose-Fermenting Yeast <i>Pachysolen tannophilus</i> (1986)

Although xylose is a major product of hydrolysis of lignocellulosic materials, few yeasts are able to convert it to ethanol. In Pachysolen tannophilus, one of the few xylose-fermenting yeasts found, aldose reductase and xylitol dehydrogenase were found to be key enzymes in the metabolic pathway for xylose fermentation. This paper presents a method for the rapid and simultaneous purification of both aldose reductase and xylitol dehydrogenase from P. tannophilus. Preliminary studies indicate that this method may be easily adapted to purify similar enzymes from other xylose-fermenting yeasts.
Towards Population Scale Activity Recognition: A Framework for Handling Data Diversity (2021)

The rising popularity of the sensor-equipped smartphone is changing the possible scale and scope of human activity inference. The diversity in user population seen in large user bases can overwhelm conventional one-size-fits-all classiﬁcation approaches. Although personalized models are better able to handle population diversity, they often require increased effort from the end user during training and are computationally expensive. In this paper, we propose an activity classification framework that is scalable and can tractably handle an increasing number of users. Scalability is achieved by maintaining distinct groups of similar users during the training process, which makes it possible to account for the differences between users without resorting to training individualized classifiers. The proposed framework keeps user burden low by leveraging crowd-sourced data labels, where simple natural language processing techniques in combination with multi-instance learning are used to handle labeling errors introduced by low-commitment everyday users. Experiment results on a large public dataset demonstrate that the framework can cope with population diversity irrespective of population size.