gebhart/patrepeval huggingface dataset:
Concise Synthesis of the Calicheamicin Oligosaccharide Using the Sulfoxide Glycosylation Method (1994)

A short synthesis of the calicheamicin oligosaccharide is reported. All the glycosidic linkages have been constructed using the sulfoxide glycosylation reaction, demonstrating the efficacy of the method. A general method to introduce N-O glycosidic linkages in oligosaccharides has been developed and employed to construct the N-O bond that connects rings A and B. In the final step of the synthesis, the two halves of the calicheamicin oligosaccharide are coupled in a completely deprotected form. This convergent synthesis permits the rapid construction of derivatives of the calicheamicin oligosaccharide to test the importance of particular structural features in DNA binding.
Rapid Screening of Phenotypic Resistance to Nevirapine by Direct Analysis of HIV Type 1 Reverse Transcriptase Activity in Plasma (1999)

Drug susceptibility testing for the clinical management of human immunodeficiency virus type 1 (HIV-1)-infected persons is often curtailed because such testing is expensive and time consuming. We describe a non-culture-based phenotypic assay for the rapid analysis of HIV-1 resistance to nevirapine. The assay measures the susceptibility of plasma reverse transcriptase (RT) activity to inhibition by nevirapine by using the PCR-based Amp-RT assay. Assay validation was made using two reference wild-type (WT) and six other nevirapine-resistant (>100-fold) HIV-1 isolates. Amp-RT IC50 values were found to correlate with those obtained by a conventional replication-based assay. The results also indicated that 50 microM nevirapine can be used in a single screening test to detect nevirapine resistance. Analysis of virus mixtures showed a detection threshold of 10% of nevirapine-resistant HIV-1 in a background of WT virus. To evaluate the assay on clinical samples, 30 plasma specimens collected longitudinally from 4 patients before and after treatment with nevirapine were analyzed, and results were compared with codon 181 genotypes. Preteatment samples and those obtained during the first 6 days of therapy (n = 21) were sensitive to nevirapine, and none had detectable Y181C mutation. Phenotypic resistance was seen in eight samples obtained after 1 week of treatment and was correlated with detection of the Y181C mutation. An increase in the level of phenotypic resistance was seen over time. These data validate this rapid and simple assay for monitoring phenotypic resistance to nevirapine.
Therapy for the mucopolysaccharidoses (2011)

Better understanding of disease pathophysiology, improved supportive care and availability of disease-specific treatments for some of the mucopolysaccharidosis (MPS) disorders have greatly improved the outlook for patients with MPS disorders. Optimal management of these multisystemic disorders involves a multidisciplinary team and regular, comprehensive follow-up. Enzyme replacement therapy (ERT) is now available for MPS I (Hurler, Hurler-Scheie and Scheie syndromes) (laronidase), MPS II (Hunter syndrome) (idursulfase) and MPS VI Maroteaux-Lamy (galsulfase), and is in development for MPS IV (Morquio syndrome) and MPS VII (Sly syndrome). Benefits of ERT can include improved walking ability, improved respiration and enhanced quality of life. Haematopoietic stem cell transplantation (HSCT) can preserve cognition and prolong survival in very young children with the most severe form of MPS I, and is under investigation for several other MPS disorders. Better tissue matching techniques, improved graft-vs-host prophylaxis and more targeted conditioning regimens have improved morbidity and mortality associated with HSCT.
Optofluidics 2013 (2013)

Optofluidics is broadly defined as the fusion of optics and microfluidics. The term optofluidics was coined less than a decade ago. Yet, the term and the concept it encapsulates have pervaded through a significant fraction of the miniature system research community. Optofluidic research continues to grow in unanticipated directions. The Second International Conference on Optofluidics (Optofluidics-2012) showcased some of these developments. The conference was first organized by Xi'an Jiaotong University in 2011 and then Suzhou University, Institute of Nanotechnology, Xi'an Jiaotong University and Suzhou Industrial Park where it was proudly hosted as a summit conference of the CHInano conference in Suzhou on 13-15 Sep 2012. We are happy that Lab on a Chip, a major publication venue for optofluidic research has scheduled this themed issue.
Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore (2017)

It is now possible to create, in a thin inorganic membrane, a single, sub-nanometer-diameter pore (i.e., a sub-nanopore) about the size of an amino acid residue. To explore the prospects for sequencing protein with it, measurements of the force and current were performed as two denatured histones, which differed by four amino acid residue substitutions, were impelled systematically through the sub-nanopore one at a time using an atomic force microscope. The force measurements revealed that once the denatured protein, stabilized by sodium dodecyl sulfate (SDS), translocated through the sub-nanopore, a disproportionately large force was required to pull it back. This was interpreted to mean that the SDS was cleaved from the protein during the translocation. The force measurements also exposed a dichotomy in the translocation kinetics: either the molecule slid nearly frictionlessly through the pore or it slipped-and-stuck. When it slid frictionlessly, regardless of whether the molecule was pulled N-terminus or C-terminus first through the pore, regular patterns were observed intermittently in the force and blockade current fluctuations that corresponded to the distance between stretched residues. Furthermore, the amplitude of the fluctuations in the current blockade were correlated with the occluded volume associated with the amino acid residues in the pore. Finally, a comparison of the patterns in the current fluctuations associated with the two practically identical histones supported the conclusion that a sub-nanopore was sensitive enough to discriminate amino acid substitutions in the sequence of a single protein molecule by measuring volumes of 0.1 nm<sup>3</sup> per read.
Adaptive Equalization and Phase Tracking for Simultaneous Analog/Digital Data Transmission (1981)

The general problem of equalization for data transmission where one of the two data sources produces continuous amplitude data samples is studied. There are various ways to configure a modem for such a transmission scheme, and we describe how a standard quadrature amplitude modulation structure can be modified to operate in this mode. This solution can be specialized to include various linear modulation schemes, such as single sideband and vestigial sideband. Theoretical analysis shows that adaptive equalization and adaptive phase tracking can be achieved with similar quality as in the familiar digital-only modem. We provide extensive computer simulation results which confirm the validity of our theory.
Request Distribution for Heterogeneous Database Server Clusters with Processing Time Estimation (2018)

Recently, data traffic on the Internet has increased due to the rapid growth of various Internet-based services. The convergence of user requests means that servers are overloaded. To solve this problem, service providers generally install multiple servers and distribute requests using a load balancer. The existing load balancing algorithms do not estimate the size of the load of unknown requests. However, the requested contents are heterogeneous and complex, so the size of the load is dependent on the servers and the contents of the requests. In this study, we propose a load balancing algorithm that distributes the requests based on estimates of the processing time, which avoids mismatches between the characteristics of servers and the request contents. The processing time for requests is estimated based on the requested contents by online machine learning, and a strategy to cover the latency of machine learning is proposed and partially conducted. To test the algorithm, we built a model of multiple database servers and performed an experiment using real log data for database requests. The simulation results showed that the proposed algorithm reduced the average processing time for requests by 94.5% compared with round robin and by 28.3% compared with least connections.
The mechanism of the β-amylase action. 1. ‘Multichain’ action on amylose (1954)

Amylose, the constituent of starch which consists essentially of unbranched glucosidic chains, is hydrolysed by ,-amylase in stepwise fashion starting from the non-reducing end. The sole fission products are maltose and continually shortening amylose chains.
Colony-stimulating factor-1 transfection of myoblasts improves the repair of failing myocardium following autologous myoblast transplantation (2008)

Autologous intramyocardial transplantation of CSF-1 overexpressing myoblasts might be a novel strategy in the treatment of ischaemia-induced heart failure.
Bit-wise Sequential Coding with Feedback (2018)

This paper considers the problem of bit-wise channel coding over a Binary Symmetric Channel (BSC) with feedback. While it is known that feedback does not increase the capacity of a memoryless channel, it is believed to simplify the coding schemes for some channels. The most significant one is the Binary Erasure Channel (BEC) where capacity is achieved by a simple sequential bit-wise repetition code under which each bit is (re-)transmitted until it is received. This sequential bit-wise feedback code has the added advantage that it can be used for streaming applications over BECs. In contrast, there is no known sequential bit-wise code with feedback that can achieve nonzero transmission rate for a BSC. For example, under Posterior Matching for a binary input channel with feedback, also known as Horstein scheme, each message is considered in its entirety in a block coding manner. This paper proposes a sequential feedback coding scheme with a nested bit-wise structure that generalizes repetition codes. This scheme is shown to achieve strictly positive rate for a large class of binary input channels including a BSC with arbitrary cross-over probability p ∈ (0, 1/2). The analysis relies on characterizing a lower bound on the step-wise Extrinsic Jensen Shannon divergence.
Goblet cell density and vascularization during conjunctival transdifferentiation. (1984)

After debridement of the entire corneal epithelium with n-heptanol, two groups of rabbit corneas were segregated according to the extent of corneal neovascularization. Using a new topographic goblet-cell counting method and routine histology, the authors have reexamined the process of conjunctival transdifferentiation and compared the changes of goblet-cell density and morphology between nonvascularized and vascularized groups for a follow-up period of 167 days. Analysis of the total goblet-cell density disclosed that no goblet cells appeared on the corneal surface during the entire period of reepithelialization. After that, two phases were identified with respect to goblet-cell density: phase I (day 0-17) and phase II (after day 17). In phase I, both groups had a similar surge of goblet cells, with the peak occurring between days 7 and 11, suggesting little correlation with vascularization. Morphologic studies indicated the presence of a prominent centripetal cellular migration. In phase II, the nonvascularized group showed a rapid decline in goblet-cell density, and as a result the morphologic transdifferentiation into a cornea-like epithelium was completed on day 43. The changes of goblet cells to a smaller size and the presence of a more acidic mucin in the centrifugal receding zone, suggested that transdifferentiation on nonvascularized corneas is a process involving changes of cellular differentiation. In contrast, the vascularized group maintained a high plateau of goblet-cell density and an epithelium with conjunctival characteristics until day 167. This result disclosed that retardation of conjunctival transdifferentiation by corneal vascularization was in phase II. The possible role of vascularization in the modulation of conjunctival transdifferentiation is discussed.
3D GIPER: global interconnect parameter extractor for full-chip global critical path analysis (2002)

A 3D Global Interconnect Parameter ExtractoR (GIPER) has been developed to provide a practical extraction tool for the full-chip global critical path analysis. It extracts the interconnect parameters (R,C) of a typical global interconnect within several minutes per net on a HP 9000/755 workstation within 5% accuracy compared to full 3D numerical simulations.
An Ethical Frame for Research with Immigrant Families (2013)

In this introduction, the editors give an overview of the ways the volume addresses the growing individual and institutional calls for increased clarity and rigor in methodological, ethical, and practical research policies and guidelines for conducting research with immigrant individuals, families, and communities. In addition to summarizing the volume's purpose, background on the U.S. immigrant population is given, followed by delineation of the five major issues contributing to the field of immigrant studies research and entering the "field" and engaging with immigrant families and communities: heterogeneity and history, documentation status, research pragmatics, research lens and bias, and influence on policy.
513. Addition reactions of heterocyclic compounds. Part XVIII. The structures and reactions of adducts from pyridines, dimethyl acetylenedicarboxylate, and carbon dioxide at low temperatures (1964)

R. M. Acheson and A. O. Plunkett, J. Chem. Soc., 1964, 2676 DOI: 10.1039/JR9640002676
Protease inhibitor coinfusion with amyloid beta-protein results in enhanced deposition and toxicity in rat brain. (1998)

Amyloid beta-protein, Abeta, is normally produced in brain and is cleared by unknown mechanisms. In Alzheimer's disease (AD), Abeta accumulates in plaque-like deposits and is implicated genetically in neurodegeneration. Here we investigate mechanisms for Abeta degradation and Abeta toxicity in vivo, focusing on the effects of Abeta40, which is the peptide that accumulates in apolipoprotein E4-associated AD. Chronic intraventricular infusion of Abeta40 into rat brain resulted in limited deposition and toxicity. Coinfusion of Abeta40 with the cysteine protease inhibitor leupeptin resulted in increased extracellular and intracellular Abeta immunoreactivity. Analysis of gliosis and TUNEL in neuron layers of the frontal and entorhinal cortex suggested that leupeptin exacerbated Abeta40 toxicity. This was supported further by the neuronal staining of cathepsin B in endosomes or lysosomes, colocalizing with intracellular Abeta immunoreactivity in pyknotic cells. Leupeptin plus Abeta40 caused limited but significant neuronal phospho-tau immunostaining in the entorhinal cortex. Intriguingly, Abeta40 plus leupeptin induced intracellular accumulation of the more toxic Abeta, Abeta42, in a small group of septal neurons. Leupeptin infusion previously has been reported to interfere with lysosomal proteolysis and to result in the accumulation of lipofuscin, dystrophic neurites, tau- and ubiquitin-positive inclusions, and structures resembling paired helical filaments. Coinfusion of Abeta40 with the serine protease inhibitor aprotinin also increased diffuse extracellular deposition but reduced astrocytosis and TUNEL and was not associated with intracellular Abeta staining. Collectively, these data suggest that an age or Alzheimer's-related defect in lysosomal/endosomal function could promote Abeta deposition and DNA fragmentation in neurons and glia similar to that found in Alzheimer's disease.
Consequences of reocclusion after successful reperfusion therapy in acute myocardial infarction. TAMI Study Group. (1990)

To determine the clinical consequences of reocclusion of an infarct-related artery after reperfusion therapy, we evaluated 810 patients with acute myocardial infarction. Patients were admitted into four sequential studies with similar entry criteria in which patency of the infarct-related artery was assessed by coronary arteriography 90 minutes after onset of thrombolytic therapy. Successful reperfusion was established acutely in 733 patients. Thrombolytic therapy included tissue-type plasminogen activator (t-PA) in 517, urokinase in 87, and a combination of t-PA and urokinase in 129 patients. All patients received aspirin, intravenous heparin and nitroglycerin, and diltiazem during the recovery phase. A repeat coronary arteriogram was performed in 88% of patients at a median of 7 days after the onset of symptoms. Reocclusion of the infarct-related artery occurred in 91 patients (12.4%), and 58% of these were symptomatic. Angiographic characteristics at 90 minutes after thrombolytic therapy that were associated with reocclusion compared with sustained coronary artery patency were right coronary infarct-related artery (65% versus 44%, respectively) and Thrombolysis in Myocardial Infarction (TIMI) flow 0 or 1 (21% versus 10%, respectively) before further intervention. Median (interquartile value) degree of stenosis in the infarct-related artery at 90 minutes was similar between groups: 99% for reoccluded (value, 90/100%) compared with 95% for patent (value, 80/99%). Patients with reocclusion had similar left ventricular ejection fractions compared with patients with sustained patency at follow-up. However, patients with reocclusion at follow-up had worse infarct-zone function at -2.7 (value, -3.2/-1.8) versus -2.4 (SD/chord) (value, -3.1/-1.3) (p = 0.016). The recovery of both global and infarct-zone function was impaired by reocclusion of the infarct-related artery compared with maintained patency; median delta ejection fraction was -2 compared with 1 (p = 0.006) and median delta infarct-zone wall motion was -0.10 compared with 0.34 SD/chord (p = 0.011), respectively. In addition, patients with reocclusion had more complicated hospital courses and higher in-hospital mortality rates (11.0% versus 4.5%, respectively; p = 0.01). We conclude that reocclusion of the infarct-related artery after successful reperfusion is associated with substantial morbidity and mortality rates. Reocclusion is also detrimental to the functional recovery of both global and infarct-zone regional left ventricular function. Thus, new strategies in the postinfarction period need to be developed to prevent reocclusion of the infarct-related artery.
SnakeToonz (2002)

SnakeToonz is an interactive system that allows children and others untrained in cel animation to create two-dimensional cartoons from video streams and images. The ability to create cartoons has traditionally been limited to professional animation houses and trained artists. SnakeToonz aims to give anyone with a video camera and a computer the ability to create compelling cel animation. This is done by combining constraints of the cartooning medium with simple user input and analysis of that input.A cartoon is created in a dialogue with the system. After recording video material the user sketches contours directly onto the first frame of video. These sketches initialize a set of spline-based active contours which are relaxed to best fit the image and other aesthetic constraints. Small gaps are closed, and the user can choose colors for the cartoon. The system then uses motion estimation techniques to track these contours through the image sequence. The user remains in the process to edit the cartoon as it progresses.
Threshold Dynamics of Singular Gravity-Capillary Waves (1996)

Surface wave experiments confirm predictions of a threshold amplitude for droplet ejection. Droplet ejection and spray originate from highly focused surface singularities in the simplest states. The threshold is found to be dependent on forcing frequency and surface tension in accordance with a simple scaling theory presented here. Linear stability analysis indicates that the dynamics of the ejections at low frequency are low dimensional. Observations confirm this, and show periodic ejections as the simplest observed state. Ejecting states at higher frequency appear turbulent in nature.
The Adenovirus E1A Repression Domain Disrupts the Interaction between the TATA Binding Protein and the TATA Box in a Manner Reversible by TFIIB (1997)

The human adenovirus E1A 243 amino acid oncoprotein possesses a transcription repression function that appears to be linked with its ability to induce cell cycle progression and to inhibit cell differentiation. The molecular mechanism of E1A repression has been poorly understood. Recently, we reported that the TATA binding protein (TBP) is a cellular target of E1A repression. Here we demonstrate that the interaction between TBP and the E1A repression domain is direct and specific. The TBP binding domain within E1A 243R maps to E1A N-terminal residues approximately 1 to 35 and is distinct from the TBP binding domain within conserved region 3 unique to the E1A 289R transactivator. An E1A protein fragment consisting of only the E1A N-terminal 80 amino acids (E1A 1-80) and containing the E1A repression function was found to block the interaction between TBP and the TATA box element as shown by gel mobility and DNase protection analysis. Interestingly, a preformed TBP-TATA box promoter complex can be dissociated by E1A 1-80. Further, TFIIB can prevent E1A disruption of TBP-TATA box interaction. TFIIB, like TBP, can overcome E1A repression of transcription in vitro. The ability of the E1A repression domain to block TBP interaction with the TATA box and the ability of TFIIB to reverse E1A disruption of the TBP-TATA box complex implies a mechanism for E1A repression distinct from those of known cellular repressors that target TBP.
Aircraft instrument Patent (1965)

Aircraft indicator for pilot control of takeoff roll, climbout path and verticle flight path in poor visibility conditions
Cell lines from xeroderma pigmentosum complementation group A lack a single-stranded-DNA-binding activity (1983)

Human fibroblasts and HeLa cells contain two major DNA-binding activities for superhelical DNA, which can be separated by phosphocellulose chromatography. The DNA-binding activity which elutes first from the column coelutes with and is probably identical to a single-stranded-DNA-binding activity. The second activity has been characterized previously. It binds preferentially to super-helical DNA containing DNA damage, but does not bind to single-stranded DNA. Five cell lines derived from patients with the repair-deficiency syndrome xeroderma pigmentosum (XP) were analyzed for the presence of these binding activities. Four of the cell lines were from the A-complementation group and one was from the D-complementation group of XP. The binding activity with preference for damaged DNA was present in all cell lines. The single-stranded-DNA-binding activity was present in the XP-D cell line but was absent or reduced in all of the four XP-A cell lines tested.
Long-term cortical recordings with microactuated microelectrodes (2007)

Current microelectrode array technologies often fail over a period of time presumably due to brain tissue reaction and micromotion around the implant site. We report here long-term cortical recordings from our novel microactuated microelectrode array technology. Our technology uses electro-thermal microactuators to move each of the three highly doped thin (~4mum thick) polysilicon microelectrodes in the array. Multi-unit activity in n=2 rodents was monitored for a period of over 12 weeks. High-quality multi-unit data with noise levels less than 10 muV peak-to-peak and signal levels ranging from 100 muV to 5 mV (peak-to-peak) were obtained over the entire duration of study. The results of this study demonstrate the long-term recording capability of the microactuated microelectrodes in rodent models.