gebhart/patrepeval huggingface dataset:
Current progress in innovative engineered antibodies (2017)

As of May 1, 2017, 74 antibody-based molecules have been approved by a regulatory authority in a major market. Additionally, there are 70 and 575 antibody-based molecules in phase III and phase I/II clinical trials, respectively. These total 719 antibody-based clinical stage molecules include 493 naked IgGs, 87 antibody-drug conjugates, 61 bispecific antibodies, 37 total Fc fusion proteins, 17 radioimmunoglobulins, 13 antibody fragments, and 11 immunocytokines. New uses for these antibodies are being discovered each year. For oncology, many of the exciting new approaches involve antibody modulation of T-cells. There are over 80 antibodies in clinical trials targeting T cell checkpoints, 26 T-cell-redirected bispecific antibodies, and 145 chimeric antigen receptor (CAR) cell-based candidates (all currently in phase I or II clinical trials), totaling more than 250 T cell interacting clinical stage antibody-based candidates. Finally, significant progress has been made recently on routes of delivery, including delivery of proteins across the blood-brain barrier, oral delivery to the gut, delivery to the cellular cytosol, and gene- and viral-based delivery of antibodies. Thus, there are currently at least 864 antibody-based clinical stage molecules or cells, with incredible diversity in how they are constructed and what activities they impart. These are followed by a next wave of novel molecules, approaches, and new methods and routes of delivery, demonstrating that the field of antibody-based biologics is very innovative and diverse in its approaches to fulfill their promise to treat unmet medical needs.
Cluster-based file replication in large-scale distributed systems (1992)

The increasing need for data sharing in large-scale distributed systems may place a heavy burden on critical resources such as file servers and networks. Our examination of the workload in one large commercial engineering environment shows that wide-spread sharing of unstable files among tens to hundreds of users is common. Traditional client-based file cacheing techniques are not scalable in such environments.
Chemically-Modified Cellulose Paper as a Microstructured Catalytic Reactor (2015)

We discuss the successful use of chemically-modified cellulose paper as a microstructured catalytic reactor for the production of useful chemicals. The chemical modification of cellulose paper was achieved using a silane-coupling technique. Amine-modified paper was directly used as a base catalyst for the Knoevenagel condensation reaction. Methacrylate-modified paper was used for the immobilization of lipase and then in nonaqueous transesterification processes. These catalytic paper materials offer high reaction efficiencies and have excellent practical properties. We suggest that the paper-specific interconnected microstructure with pulp fiber networks provides fast mixing of the reactants and efficient transport of the reactants to the catalytically-active sites. This concept is expected to be a promising route to green and sustainable chemistry.
Predicting customer loyalty (2015)

The Investment Department of ING asked us to build a model that predicts customer loyalty using the Net Promoter Score (NPS) system and a dashboard that would show the results of the model. With this model and dashboard ING may be able to get an insight into which groups of customers are at risk to complain.
Giant Polymerlike Micelles Formed by Nucleoside-Functionalized Lipids (2002)

We report an investigation on the aggregation of 1,2-dilauroyl-sn-glycero-3-phosphatidyluridine (DLPU), a surfactant molecule that merges the self-assembling properties of lecithins with the molecular recognition characteristics of nucleic bases in a phosphate-buffered aqueous solution at physiological pH and as a function of lipid concentration. Because spontaneous self-assembly and interfacial properties are the result of a delicate balance between hydrophobic interactions and polar-head interactions, a structural characterization is essential for a complete and full understanding of base−base properties in the aggregates, as observed by spectroscopic techniques. Small-angle neutron scattering, static light scattering, and quasi-elastic light scattering have been employed to assess the structural evolution of the binary system as the lipid concentration is increased. The data indicate the presence of rather flexible elongated aggregates, whose local structure is cylindrical and remains essentially unchanged during micellar growth. Scattering data are fully supported by cryo-TEM analysis. The results are consistent with micellar unidimensional growth to giant wormlike aggregates that eventually entangle to form a transient network with a response to mechanical stress that is similar to that of polymer solutions in the semidilute range. Such aggregates are known as polymerlike micelles to stress the similarity with the behavior of macromolecules in good solvents. In our case, the correspondence is not limited to a mesosocopic structural scale because from a chemical point of view each monomer contains a nucleic acid functionality that is also expressed in the polymerlike aggregates whose biopolymeric counterpart is in fact a polynucleotide. Therefore, these new aggregates can be considered to be the first example of an “associative polynucleotide”.
Metabolomics, at the heart (2020)

Physiology
With heart failure a leading cause of death, a better understanding of metabolic function in the heart is a welcome advance. Murashige et al. measured more than 270 metabolites using liquid chromatography–mass spectrometry in human blood samples taken from an artery entering the heart and from a vein leaving it. Differences thus reflected the metabolic processes at work in the heart. Their results confirmed that hearts voraciously consume fatty acids. Hearts secreted, rather than consumed, amino acids, thus revealing active proteolysis. In patients with heart failure, ketone and lactate consumption increased, as did proteolysis. These findings could lead to strategies for fighting heart disease by altering metabolism.

Science , this issue p. [364][1]

 [1]: /lookup/doi/10.1126/science.abc8861
Increased Neutrophil Extracellular Trap–Mediated Staphylococcus aureus Clearance Through Inhibition of Nuclease Activity by Clindamycin and Immunoglobulin (2014)

The Gram-positive human pathogen Staphylococcus aureus causes a variety of human diseases such as skin infections, pneumonia, and endocarditis. The micrococcal nuclease Nuc1 is one of the major S. aureus virulence factors and allows the bacterium to avoid neutrophil extracellular trap (NET)-mediated killing. We found that addition of the protein synthesis inhibitor clindamycin to S. aureus LAC cultures decreased nuc1 transcription and subsequently blunted nuclease activity in a molecular beacon-based fluorescence assay. We also observed reduced NET degradation through Nuc1 inhibition translating into increased NET-mediated clearance. Similarly, pooled human immunoglobulin specifically inhibited nuclease activity in a concentration-dependent manner. Inhibition of nuclease activity by clindamycin and immunoglobulin enhanced S. aureus clearance and should be considered in the treatment of S. aureus infections.
Enabling Efficient Hypervisor-as-a-Service Clouds with Ephemeral Virtualization (2016)

When considering a hypervisor, cloud providers must balance conflicting requirements for simple, secure code bases with more complex, feature-filled offerings. This paper introduces Dichotomy, a new two-layer cloud architecture in which the roles of the hypervisor are split. The cloud provider runs a lean hyperplexor that has the sole task of multiplexing hardware and running more substantial hypervisors (called featurevisors) that implement features. Cloud users choose featurevisors from a selection of lightly-modified hypervisors potentially offered by third-parties in an "as-a-service" model for each VM. Rather than running the featurevisor directly on the hyperplexor using nested virtualization, Dichotomy uses a new virtualization technique called eemeral virtualization which efficiently (and repeatedly) transfers control of a VM between the hyperplexor and featurevisor using memory mapping techniques. Nesting overhead is only incurred when the VM is accessed by the featurevisor. We have implemented Dichotomy in KVM/QEMU and demonstrate average switching times of 80 ms, two to three orders of magnitude faster than live VM migration. We show that, for the featurevisor applications we evaluated, VMs hosted in Dichotomy deliver up to 12% better performance than those hosted on nested hypervisors, and continue to show benefit even when the featurevisor applications run as often as every 2.5~seconds.
Diffractive optical elements for high gain lasers with arbitrary output beam profiles (2007)

We introduce a previously unreported laser cavity configuration, using a diffractive optical element (DOE) in place of the output coupler. Such a configuration allows the DOE to work both in reflection, as a mode shaping element, and in transmission as a beam shaper. Employing dual wavelength DOE optimization techniques and phase delays greater than 2pi, allows the two functions to be designed independently. Thus, an arbitrary output beam profile can be combined with a mode shape which maximizes energy extraction from the gain medium. Devices are designed and their performance modeled for a 1m cavity with 5mm diameter mirrors and a wavelength of 632.8nm. An element with 32 quantization levels and a maximum phase delay of 8pi in transmission produces high quality results.
Intrapartum fetal scalp lactate sampling for fetal assessment in the presence of a non-reassuring fetal heart rate trace (2015)

When further testing to assess fetal well-being in labour is indicated, fetal scalp blood lactate estimation is more likely to be successfully undertaken than pH estimation. Further studies may consider subgroup analysis by gestational age, the stage of labour and sampling within a prolonged second stage of labour. Additionally, we await the findings from the ongoing studies that compare allocation to no fetal blood sample with sampling for lactate and address longer-term neonatal outcomes, maternal satisfaction with intrapartum fetal monitoring and an economic analysis.
Treatment with marine collagen peptides modulates glucose and lipid metabolism in Chinese patients with type 2 diabetes mellitus (2010)

This study was aimed at examining the therapeutic effects of marine collagen peptides (MCPs) from fish hydrolysate in Chinese patients with type 2 diabetes mellitus (T2DM). A total of 100 diabetic patients and 50 healthy controls were recruited. Diabetic patients were randomized into treatment and control groups. The patients in the treatment group received an additional 13 g of MCPs daily for 3 months. Their blood samples were collected before, and 1.5 and 3 months after, treatment to evaluate glucose and lipid metabolism. The levels of serum high-sensitivity C-reactive protein (hs-CRP), nitric oxide (NO), bradykinin, prostacyclin (PGI2), and adipokines were determined. Significantly reduced levels of fasting blood glucose, human glycated hemoglobin A1c (GHbA1c), fasting blood insulin, total triglycerides, total cholesterol, low-density lipoprotein, and free-fatty acids, but increased levels of insulin sensitivity index and HDL were observed in T2DM patients following treatment with MCPs for 1.5 and 3 months. The values of these measures were significantly lower or higher than those of patient controls (p < 0.01), respectively. Interestingly, significantly decreased levels of hs-CRP and NO, but increased levels of bradykinin, PGI2, and adiponectin were detected in MCP-treated T2DM patients (p < 0.01), as compared with their basal values or the levels in patient controls. MCP treatment improved glucose and lipid metabolism in diabetic patients.
50Gb/s Hybrid Integrated Si-Photonic Optical Link in 16nm FinFET (2020)

We present an EAM based single-mode optical link. The TX uses over-peaking to improve modulation efficiency and relax TIA's noise requirement. The RX uses a 3-stage TIA with T-coils to improve bandwidth. The link achieves <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$BER < 10^{-12}$</tex> while consuming 4.31pJ/bit at 50Gb/s with 2dB link margin.
Peroxisome Proliferator-activated Receptor γ and Ligands Inhibit Surfactant Protein B Gene Expression in the Lung (2003)

Pulmonary nonciliated bronchiolar epithelial cells (Clara cells) and alveolar type II (AT II) epithelial cells are responsible for surfactant synthesis and secretion. These cells are highly lipogenic with a high lipid turnover rate. Although only 10% of surfactant lipids are neutral lipids, they play very important roles in maintaining pulmonary surfactant homeostasis. Many metabolic intermediate products of neutral lipids serve as ligands for various nuclear receptors that bind to target genes to influence gene transcription. In this report, the functional role of the neutral lipid metabolites, 15-deoxy-Delta12,14-prostaglandin J2 and 9-hydroxyoctadecanoic acids, and peroxisome proliferator-activated receptor gamma was evaluated in surfactant protein B gene regulation. These reagents down-regulated surfactant protein B gene expression in respiratory epithelial cells at the transcriptional level in both cell line and whole lung explant systems. The studies support the concept that surfactant protein B homeostasis is influenced by neutral lipid metabolites in the lung.
A low-offset high-speed double-tail dual-rail dynamic latched comparator (2010)

This paper presents a new dynamic latched comparator which shows lower input-referred latch offset voltage and higher load drivability than the conventional dynamic latched comparators. With two additional inverters inserted between the input- and output-stage of the conventional double-tail dynamic comparator, the gain preceding the regenerative latch stage was improved and the complementary version of the output-latch stage, which has bigger output drive current capability at the same area, was implemented. As a result, the circuit shows up to 25% less input-referred latch offset voltage and 44% less sensitivity of the delay versus the input voltage difference (delay/log(ΔVin)), which is about 17.2ps/decade, than the conventional double-tail latched comparator at approximately the same area and power consumption.
High-Stabilization 85 W All-Solid-State Green Laser Operation (2004)

This paper reported high power high stabilization 85 W all solid state green laser operation, which was pumped by 80×20 W high power laser arrays. The theoretical analysis of the influence of thermal effect and phase mismatching about frequency doubling crystal on output was presented. The calorific power distribution is numerically simulated and the values of frequency doubling crystal phase mismatching varying with the change of temperature were given. In experiment, double acousto optic Q switching were employed inside single Nd∶YAG rod, high efficiency flat concave intracavity frequency doubled resonance structure. A maximum green power of 85 W was generated at 20.4 kHz repetition rate and 230 ns pulse width when pumped current of laser diodes was 17.3 A with compensating phase mismatch by angle departuring and strong cooling big KTP crystal, leading to ±1.03% instability and 9.7% of optical optical conversion efficiency.
New analysis of a reciprocal Left Hand Circular Polarization Selective Surface (LHCPSS) (2009)

This paper presents the results from analyzing Pierrot's LHCPSS with the numerical technique presented in [1]. In contrast to the results presented in [2] from analyzing a similar LHCPSS design with the full-wave EM solver NEC (a MoM technique), this numerical technique does not rely on calibrating the results against the results of a PEC plate of the same transverse dimensions in order to eliminate the effect of the diffraction that occurs at the edge of the finite-size structure under a single monochromatic plane wave illumination. The technique eliminates the effect of the diffraction by using a Maxwellian tapered beam of dominant polarization, focused at the center of the finite-size structure. As this beam consists of a summation of many incident propagating plane waves, the technique provides the results over a wide range of incidence angle values in a single application. When implemented with the FDTD, the technique also takes into account the presence of dielectric material, which NEC cannot do. Since the edge is not illuminated, the thickness of the structure does not degrade the accuracy of the results. The results of Pierrot's LHCPSS presented herein are deemed to be accurate over the incidence range of about 0 les thetas <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sup> les 60deg in the xz plane passing through the center of the LHCPSS.
Indoor-ALPS (2014)

Location prediction enables us to use a person's mobility history to realize various applications such as efficient temperature control, opportunistic meeting support, and automated receptionists. Indoor location prediction is a challenging problem, particularly due to a high density of possible locations and short transition distances between these locations. In this paper we present Indoor-ALPS, an Adaptive Indoor Location Prediction System that uses temporal-spatial features to create individual daily models for the prediction of when a user will leave their current location (transition time) and the next location she will transition to. We tested Indoor-ALPS on the Augsburg Indoor Location Tracking Benchmark and compared our approach to the best performing temporal-spatial mobility prediction algorithm, Prediction by Partial Match (PPM). Our results show that Indoor-ALPS improves the temporal-spatial prediction accuracy over PPM for look-aheads up to 90 minutes by 6.2%, and for up to 30 minute look-aheads by 10.7%. These results demonstrate that Indoor-ALPS can be used to support a wide variety of indoor mobility prediction-based applications.
Interleukin-7 Facilitates HIV-1 Transmission to Cervico-Vaginal Tissue ex vivo (2013)

The majority of HIV-1 infections in women occur through vaginal intercourse, in which virus-containing semen is deposited on the cervico-vaginal mucosa. Semen is more than a mere carrier of HIV-1, since it contains many biological factors, in particular cytokines, that may affect HIV-1 transmission. The concentration of interleukin (IL)-7, one of the most prominent cytokines in semen of healthy individuals, is further increased in semen of HIV-1-infected men. Here, we investigated the potential role of IL-7 in HIV-1 vaginal transmission in an ex vivo system of human cervico-vaginal tissue. We simulated an in vivo situation by depositing HIV-1 on cervico-vaginal tissue in combination with IL-7 at concentrations comparable with those measured in semen of HIV-1-infected individuals. We found that IL-7 significantly enhanced virus replication in ex vivo infected cervico-vaginal tissue. Similarly, we observed an enhancement of HIV-1 replication in lymphoid tissue explants. Analysis of T cells isolated from infected tissues showed that IL-7 reduced CD4⁺ T cell depletion preventing apoptosis, as shown by the decrease in the number of cells expressing the apoptotic marker APO2.7 and the increase in the expression of the anti-apoptotic protein B-cell lymphoma (Bcl)-2. Also, IL-7 increased the fraction of cycling CD4⁺ T cells, as evidenced by staining for the nuclear factor Ki-67. High levels of seminal IL-7 in vivo may be relevant to the survival of the founder pool of HIV-1-infected cells in the cervico-vaginal mucosa at the initial stage of infection, promoting local expansion and dissemination of HIV infection.
Childhood-onset schizophrenia/autistic disorder and t(1;7) reciprocal translocation: Identification of a BAC contig spanning the translocation breakpoint at 7q21 (2000)

Childhood-onset schizophrenia (COS) is defined by the development of first psychotic symptoms by age 12. While recruiting patients with COS refractory to conventional treatments for a trial of atypical antipsychotic drugs, we discovered a unique case who has a familial t(1;7)(p22;q21) reciprocal translocation and onset of psychosis at age 9. The patient also has symptoms of autistic disorder, which are usually transient before the first psychotic episode among 40-50% of the childhood schizophrenics but has persisted in him even after the remission of psychosis. Cosegregating with the translocation, among the carriers in the family available for the study, are other significant psychopathologies, including alcohol/drug abuse, severe impulsivity, and paranoid personality and language delay. This case may provide a model for understanding the genetic basis of schizophrenia or autism. Here we report the progress toward characterization of genomic organization across the translocation breakpoint at 7q21. The polymorphic markers, D7S630/D7S492 and D7S2410/D7S646, immediately flanking the breakpoint, may be useful for further confirming the genetic linkage for schizophrenia or autism in this region. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:749-753, 2000. Published 2000 Wiley-Liss, Inc.
Heat shock protein 27 is associated with decreased survival in node-negative breast cancer patients. (2005)

The expression of hsp27 in primary breast cancers is associated with a short survival for node-negative patients.
Composing Multi-Ported Memories on FPGAs (2014)

Multi-ported memories are challenging to implement on FPGAs since the block RAMs included in the fabric typically have only two ports. Hence we must construct memories requiring more than two ports, either out of logic elements or by combining multiple block RAMs. We present a thorough exploration and evaluation of the design space of FPGA-based soft multi-ported memories for conventional solutions, and also for the recently proposed Live Value Table (LVT) [LaForest and Steffan 2010] and XOR [LaForest et al. 2012] approaches to unidirectional port memories, reporting results for both Altera and Xilinx FPGAs. Additionally, we thoroughly evaluate and compare with a recent LVT-based approach to bidirectional port memories [Choi et al. 2012].
Identification and Characterization of a Membrane Receptor for Proteolysis-Inducing Factor on Skeletal Muscle (2007)

Proteolysis-inducing factor (PIF) is a sulfated glycoprotein produced by cachexia-inducing tumors, which induces atrophy of skeletal muscle. PIF has been shown to bind specifically with high affinity (K(d), in nanomolar) to sarcolemma membranes from skeletal muscle of both the mouse and the pig, as well as murine myoblasts and a human muscle cell line. Ligand binding was abolished after enzymatic deglycosylation, suggesting that binding was mediated through the oligosaccharide chains in PIF. Chondroitin sulfate, but not heparan or dermatan sulfate, showed competitive inhibition (K(d), 1.1 x 10(-7) mol/L) of binding of PIF to the receptor, suggesting an interaction with the sulfated oligosaccharide chains. Ligand blotting of [(35)S]PIF to triton solublized membranes from C(2)C(12) cells provided evidence for a binding protein of apparent M(r) of approximately 40,000. Amino acid sequence analysis showed the PIF receptor to be a DING protein. Antisera reactive to a 19mer from the N-terminal amino acid residues of the binding protein attenuated protein degradation and activation of the ubiquitin-proteasome pathway induced by PIF in murine myotubes. In addition, the antisera was highly effective in attenuating the decrease in body weight in mice bearing the MAC16 tumor, with a significant increase in muscle wet weight due to an increase in the rate of protein synthesis, together with a reduction in protein degradation through attenuation of the increased proteasome expression and activity. These results confirm that the PIF binding protein has a functional role in muscle protein atrophy in cachexia and that it represents a potential new therapeutic target.