gebhart/patrepeval huggingface dataset:
Poly(hydrophobic Amino Acids) and Liposomes for Delivery of Vaccine against Group A Streptococcus (2022)

Adjuvants and delivery systems are essential components of vaccines to increase immunogenicity against target antigens, particularly for peptide epitopes (poor immunogens). Emulsions, nanoparticles, and liposomes are commonly used as a delivery system for peptide-based vaccines. A Poly(hydrophobic amino acids) delivery system was previously conjugated to Group A Streptococcus (GAS)-derived peptide epitopes, allowing the conjugates to self-assemble into nanoparticles with self adjuvanting ability. Their hydrophobic amino acid tail also serves as an anchoring moiety for the peptide epitope, enabling it to be integrated into the liposome bilayer, to further boost the immunological responses. Polyleucine-based conjugates were anchored to cationic liposomes using the film hydration method and administered to mice subcutaneously. The polyleucine-peptide conjugate, its liposomal formulation, and simple liposomal encapsulation of GAS peptide epitope induced mucosal (saliva IgG) and systemic (serum IgG, IgG1 and IgG2c) immunity in mice. Polyleucine acted as a potent liposome anchoring portion, which stimulated the production of highly opsonic antibodies. The absence of polyleucine in the liposomal formulation (encapsulated GAS peptide) induced high levels of antibody titers, but with poor opsonic ability against GAS bacteria. However, the liposomal formulation of the conjugated vaccine was no more effective than conjugates alone self-assembled into nanoparticles.
Relief analysis and extraction (2009)

We present an approach for extracting reliefs and details from relief surfaces. We consider a relief surface as a surface composed of two components: a base surface and a height function which is defined over this base. However, since the base surface is unknown, the decoupling of these components is a challenge. We show how to estimate a robust height function over the base, without explicitly extracting the base surface. This height function is utilized to separate the relief from the base. Several applications benefiting from this extraction are demonstrated, including relief segmentation, detail exaggeration and dampening, copying of details from one object to another, and curve drawing on meshes.
Definition and refinement of chromosome 8p regions of loss of heterozygosity in gastric cancer. (2000)

Loss of heterozygosity at several chromosomal loci is a common feature of the malignant progression of human tumors. These regions are thought to harbor one or more putative tumor suppressor gene(s) playing a role in tumor development. Allelic losses on the short arm of chromosome 8 (8p) have been reported as frequent events in several cancers, and three commonly deleted regions have been defined at 8p11.2-12, 8p21-22, and 8p23.1. To evaluate the possible involvement of these regions in gastric cancer, we used eight microsatellite markers to perform an extensive analysis of allele loss at 8p21-22 in 52 cases of primary gastric adenocarcinoma. We found that 44% of tumors showed allelic loss for at least one marker at 8p21-22. The critical region of loss was found to be between markers LPL and D8S258, which displayed loss of heterozygosity in 39% and 33% of cases, respectively. This region is centromeric to the LPL locus and centered on the D8S258 locus. We conclude that 8p22 deletion is a frequent event in gastric cancer and suggest the presence of a putative tumor suppressor gene near the D8S258 locus. Initial steps were taken toward the identification of this gene, which is likely to play an important role in the pathogenesis of gastric cancer and of other tumors as well.
Identification of circRNAs linked to Alzheimer’s disease and related dementias (2022)

Abstract Background Although linear mRNA transcriptome study has been well performed for Alzheimer’s disease (AD), little is known for the non‐coding RNA. Circular RNAs(circRNAs) are particularly notable because of their selective expression in the brain and differential regulation in neurological disease conditions, including AD. CircRNAs are formed from back‐splicing events, and they majorly function as sponges for microRNA and RNA‐binding proteins. Our study examines circRNA expression patterns associated with AD and related dementias in different brain regions. Method To detect and quantify cortical circRNAs, we used Mount Sinai Brain Bank (MSBB) rRNA‐depleted RNA sequencing(RNAseq) data derived from inferior frontal gyrus tissue of 278 subjects(216 AD cases, 62 controls) by applying DCC and Circexplor3. To detect hippocampal circRNAs, we generated rRNA‐depleted RNAseq data from 207 human postmortem hippocampal region samples(186 AD, 21 controls) obtained from the BU Alzheimer Disease Research Center. Differentially expressed circRNAs were identified using limma and DESeq2. Both cortical and hippocampal circRNA candidates were further validated using RT‐qPCR in a smaller independent cohort of patients. Result We identified over 300 circRNA significantly associated with AD condition (FDR&lt;0.05). Interestingly, a major fraction of these circRNAs are derived from genes involved in excitatory synaptic transmission, axon guidance, and calcium signaling pathways. CircRNA from AD‐linked genes, including APP, PICALM and PSEN1, were identified as top candidates associated with AD in cortex. In the hippocampus, we find circSLC8A1 and circHOMER1 among the top differentially regulated circRNAs. We also find expression of circHOMER1, circMLIP, circATRNL1 among others to be correlated with AD traits of clinical dementia, BRAAK pathology, and amyloid plaque. Our analysis of AD‐only patients and AD patients with vascular or Lewy body dementia revealed differential expression of 39 circRNAs common among all three disease conditions. Conclusion CircRNAs are a novel class of regulatory RNAs but their role in AD pathogenesis is just beginning to be explored. Our study identified circRNA whose expression is linked to AD and are correlated with indices of tauopathy and cognitive loss in cortex and hippocampus. Furthermore, particular circRNAs were differentially expressed among patients with AD or other dementias, suggesting that circRNA might be useful disease biomarkers or targets for disease intervention.
Extraction of Old Pacemaker or Cardioverter-Defibrillator Leads by Laser Sheath Versus Femoral Approach (2010)

Old transvenous leads were extracted with similar success and complication rates by the femoral and laser approaches. However, the femoral approach was associated with longer procedures and a longer duration of fluoroscopic exposure.
Rhenium Complexes with Visible‐Light‐Induced Anticancer Activity (2013)

Shedding light on the matter: Rhenium(I) indolato complexes with highly potent visible-light-triggered antiproliferative activity (complex 1: EC50 light=0.1 μM vs EC50 dark=100 μM) in 2D- and 3D-organized cancer cells are reported and can be traced back to an efficient generation of singlet oxygen, causing rapid morphological changes and an induction of apoptosis.
A Mitotic Phosphorylation Feedback Network Connects Cdk1, Plk1, 53BP1, and Chk2 to Inactivate the G2/M DNA Damage Checkpoint (2010)

DNA damage checkpoints arrest cell cycle progression to facilitate DNA repair. The ability to survive genotoxic insults depends not only on the initiation of cell cycle checkpoints but also on checkpoint maintenance. While activation of DNA damage checkpoints has been studied extensively, molecular mechanisms involved in sustaining and ultimately inactivating cell cycle checkpoints are largely unknown. Here, we explored feedback mechanisms that control the maintenance and termination of checkpoint function by computationally identifying an evolutionary conserved mitotic phosphorylation network within the DNA damage response. We demonstrate that the non-enzymatic checkpoint adaptor protein 53BP1 is an in vivo target of the cell cycle kinases Cyclin-dependent kinase-1 and Polo-like kinase-1 (Plk1). We show that Plk1 binds 53BP1 during mitosis and that this interaction is required for proper inactivation of the DNA damage checkpoint. 53BP1 mutants that are unable to bind Plk1 fail to restart the cell cycle after ionizing radiation-mediated cell cycle arrest. Importantly, we show that Plk1 also phosphorylates the 53BP1-binding checkpoint kinase Chk2 to inactivate its FHA domain and inhibit its kinase activity in mammalian cells. Thus, a mitotic kinase-mediated negative feedback loop regulates the ATM-Chk2 branch of the DNA damage signaling network by phosphorylating conserved sites in 53BP1 and Chk2 to inactivate checkpoint signaling and control checkpoint duration.
Polylactones 57. Biodegradable Networks Based on A−B−A Triblock Segments Containing Poly(Ethylene Glycol)sSyntheses and Drug Release Properties (2003)

Condensation of Bu(2)Sn(OMe)(2) with poly(ethylene glycol)s yielded macrocyclic tin alkoxides which were, in turn, used as cyclic initiators for the ring-expansion polymerization of epsilon-caprolactone, D,L-lactide, or trimethylene carbonate. The resulting cyclic triblock copolymers were in situ cross-linked with trimesoyl chloride. The lengths of the A-B-A triblock segments were varied via the monomer-initiator ratio (M/I) or via the lengths of the poly(ethylene glycol)s. After extraction with CH(2)Cl(2), the isolated networks were characterized by (1)H NMR spectroscopy, DSC measurements, and swelling experiments. The release of dexamethasone and 5-fluorouracil from two triblock networks was studied in physiological buffer solutions at 37 degrees C over a period of several weeks. A strong initial burst was found in all cases. Only a weak initial burst and a more continuous release was observed when networks of random L-lactide/epsilon-caprolactone copolymers were studied under the same conditions.
Protective role of brain derived neurotrophic factor (BDNF) in obstructive sleep apnea syndrome (OSAS) patients (2020)

Obstructive sleep apnea syndrome (OSAS) is a common disorder characterized by repeated episodes of upper airways collapse during the sleep. The following intermittent hypoxia triggers a state of chronic inflammation, which also interests the nervous system leading to neuronal damage and increased risk of cognitive impairment. Brain derived neurotrophic factor (BDNF) is a growth factor often associated with neuroplasticity and neuroprotection whose levels increase in several condition associated with neuronal damage. However, whether patients affected by OSAS have altered BDNF levels and whether such alteration may be reflective of their cognitive impairment is still controversial. Here we show that, when compared to healthy control volunteers, OSAS patients have increased serum levels of BDNF. Moreover, OSAS patients with the higher levels of BDNF also have reduced neurocognitive impairment as measured by The Montreal Cognitive Assessment (MoCA) questionnaire. Treatment with standard non-invasive mechanical ventilation (CPAP) also was able to ameliorate the level of cognitive impairment. Altogether our results indicate that BDNF levels represent a neuroprotective response to intermittent hypoxia in OSAS patients.
ATP11B mediates platinum resistance in ovarian cancer (2021)

Additionally, the empty liposome and control siRNA PCNA-stained panels were noted to appear to be the same. An institutional review committee concluded that the errors in Figure The authors provided the correct version of Figure That correct version is shown below.
Antibody Response of Dogs After Immunisation with Chimeric Vaccine Against Borreliosis (2015)

Two chimeric recombinant fusion proteins (ch-rOspC and ch-rOspA) were created. They are composed of the immunodominant domains of OspC and OspA proteins described in the clinically most important strains of Borrelia. The gene constructs for these chimeric proteins were inserted into plasmids pET28 allowing induced gene expressions in a bacterial system. The proteins were expressed in E. coli BL21 strains, purified and used for preparation of the vaccine. One dose of the tested vaccines contained 50 μg of each relevant protein (ch-rOspC, ch-rOspA, or ch-rOspC + ch-rOspA). PET GEL A (Seppic) or Aluminium hydroxide gel as the immune adjuvants were used. The dogs were vaccinated three times at 21 days intervals subcutaneously or intradermally and unvaccinated controls were also included. The vaccine-elicited serum action antibodies specific to OspA and OspC were determined using in-house ELISA sets. The immunisation induced specific antibody response in the vaccinated animals and OspC and OspA from representative genospecies B. garinii , B. afzelii , and B. burgdorferi sensu stricto were recognized. The control dogs were without antibody response. ELISA examination enables determination of specific post-vaccination antibodies against OspA and OspC. Detection of these antibodies and their quantification may be used for evaluation of efficiency of vaccines.
Polyclonal Rabbit Antisera that Detect the Vpr Protein of SIV SM and SIV MAC on Immunoblots of Purified Virions (1995)

Antisera suitable for detection of SIVSM or SIVMAC Vpr proteins on Western blots of purified virions are currently not available. We have expressed the Vpr protein of SIVSMPBj1.9 in a gst-based prokaryotic expression system and used it to raise polyclonal antisera in rabbits. Two immune sera were obtained that specifically recognized both cell- and virion-associated Vpr protein on immunoblots of three different SIV isolates (SIVSMPBj1.9, SIVMACBK28, and SIVMAC239). Because Vpr is believed to play an important role in HIV/SIV replication and pathogenesis, these reagents will allow the extension of functional analyses of this protein to a broader spectrum of viruses. Both antisera and the gst-Vpr expression plasmid have been submitted to the NIAID AIDS Research and Reagent Program and are available to interested investigators.
Direct Recognition of Superparamagnetic Nanocrystals by Macrophage Scavenger Receptor SR-AI (2013)

Scavenger receptors (SRs) are molecular pattern recognition receptors that have been shown to mediate opsonin-independent uptake of therapeutic and imaging nanoparticles, underlying the importance of SRs in nanomedicine. Unlike pathogens, engineered nanomaterials offer great flexibility in control of surface properties, allowing addressing specific questions regarding the molecular mechanisms of nanoparticle recognition. Recently, we showed that SR-type AI/II mediates opsonin-independent internalization of dextran superparamagnetic iron oxide (SPIO) nanoparticles via positively charged extracellular collagen-like domain. To understand the mechanism of opsonin-independent SPIO recognition, we tested the binding and uptake of nanoparticles with different surface coatings by SR-AI. SPIO coated with 10 kDa dextran was efficiently recognized and taken up by SR-AI transfected cells and J774 macrophages, while SPIO with 20 kDa dextran coating or cross-linked dextran hydrogel avoided the binding and uptake. Nanoparticle negative charge density and zeta-potential did not correlate with SR-AI binding/uptake efficiency. Additional experiments and computer modeling revealed that recognition of the iron oxide crystalline core by the positively charged collagen-like domain of SR-AI is sterically hindered by surface polymer coating. Importantly, the modeling revealed a strong complementarity between the surface Fe-OH groups of the magnetite crystal and the charged lysines of the collagen-like domain of SR-AI, suggesting a specific recognition of SPIO crystalline surface. These data provide an insight into the molecular recognition of nanocrystals by innate immunity receptors and the mechanisms whereby polymer coatings promote immune evasion.
Performance of silicon solar cells under filtered spectra and different light intensities (2017)

10.7567/JJAP.56.08MC13
The bilateral pedicle flap-tunnel technique: a new approach to cover connective tissue grafts. (1999)

A new surgical technique for the treatment of adjacent soft tissue marginal recession is presented. This technique combines the use of a tunnel procedure with double lateral pedicle flaps to cover a connective tissue graft. This approach combines the advantages of the tunnel technique with the increased blood supply and protection provided by pedicle flaps. Indications include adjacent Class I and II deep, wide recessions; however, the procedure may also be applied to mild Class III recessions. Two case reports are presented to illustrate this new technique.
Mechanical design of Altair, the Gemini-North adaptive optics system (2000)

Altair is the facility adaptive optics system for the Gemini-North 8-meter Telescope. This paper gives an overview of the key mechanical systems and feature of Altair including the optical bench assembly mechanics and opto- mechanics, the instrument structure, and the electronics enclosure.
Helix unwinding process in the chiral smectic C phase of MHPOBC as observed by conoscopy (2003)

Conoscopic studies have been made on the helix unwinding process in the chiral smectic C phase of MHPOBC. The unwinding process is rather unique in the sense that abrupt changes of the biaxiality and apparent tilt angle are followed by further gradual changes before the complete helix unwinding. The process is qualitatively explained by simulating the conoscopic images using the 4 x 4 matrix method with consideration of model molecular distributions, by taking account of both the ferroelectric and dielectric coupling between molecules and a field. The transmittance loss due to selective reflection was also measured under the application of a stepwise d.c. field. The shift of the dip position due to the loss, toward a longer wavelength region, was observed at low field. In contrast, the emergence of a transmittance loss at the same wavelength as that of an unperturbed state was observed. This phenomenon is explained by the ferroelectric deformation of a helix with the pitch unchanged.
Adhesion selectivity by electrostatic complementarity. I. One-dimensional stripes of charge (2011)

Highly enhanced and selective adhesion can be achieved between surfaces patterned with charges even when each one has no net charge. In this and a companion paper [C. Jin, Y. Bai, A. Jagota, and C.-Y. Hui, J. Appl. Phys. 110, 054903 (2011)] we analyze the possibility of adhesion selectivity between two flat surfaces patterned with stripes of surface charge chosen such that each surface initially carries no net charge. A few combinations, with appropriately matching strip widths, are predicted to adhere to each other. We also find that the deformability of the materials plays a critical role in defining the range of patterns that recognize each other, i.e., their selectivity. With increasing compliance, a significant enhancement of adhesion can be achieved by deformation that allows better matching between charge patterns.
Rapid Prototyping of Microstructures by Soft Lithography for Biotechnology (2009)

This chapter describes the methods and specific procedures used to fabricate microstructures by soft lithography. These techniques are useful for the prototyping of devices useful for applications in biotechnology. Fabrication by soft lithography does not require specialized or expensive equipment; the materials and facilities necessary are found commonly in biological and chemical laboratories in both academia and industry. The combination of the fact that the materials are low-cost and that the time from design to prototype device can be short (< 24 h) makes it possible to use and to screen rapidly devices that also can be disposable. Here we describe the procedures for fabricating microstructures with lateral dimensions as small as 1 mum. These types of microstructures are useful for microfluidic devices, cell-based assays, and bioengineered surfaces.
Compact and High Performance Torque-Controlled Actuators and its Implementation to Disaster Response Robot (2018)

Applying robots in narrow and cluttered disaster environments such as oil refineries requires a slim body and a wide range of motion. It is also necessary to have abilities to absorb unexpected contact with the environment and to walk on scattered debris. In this paper we propose new compact and high performance torque-controlled actuators for legged robots to satisfy the above mentioned requirements. For axial compactness, torque sensors are designed as ring-shaped thin cylinders surrounding motors or gears with strain gauges for sensing. To achieve broad bandwidth of torque control, we introduced an analog differentiator circuit into an analog digital converter (ADC) board in order to suppress noise in the differential control of joint torque. We also propose methods to reduce torque ripple caused by the deformation of the harmonic drive gear and electromagnetic interference (EMI) from a motor and a motor driver. Finally, experiments of a collision with objects and movement on scattered debris were executed with a fully torque-controlled legged robot built with the proposed actuators.
A 1.54mW/Element 150μm-Pitch-Matched Receiver ASIC with Element-Level SAR/Shared-Single-Slope Hybrid ADCs for Miniature 3D Ultrasound Probes (2019)

This paper presents an ultrasound receiver ASIC in 180nm CMOS that enables element-level digitization of echo signals in miniature 3D ultrasound probes. It is the first to integrate an analog front-end and a 10-b Nyquist ADC within the 150 μm element pitch of a 5-MHz 2D transducer array. To achieve this, a hybrid SAR/shared-single-slope architecture is proposed in which the ramp generator is shared within each 2x2 subarray. The ASIC consumes 1.54mW/element and has been successfully demonstrated in an acoustic imaging experiment.
Path toward manufacturable superconducting qubits with relaxation times exceeding 0.1 ms (2022)

Abstract As the superconducting qubit platform matures towards ever-larger scales in the race towards a practical quantum computer, limitations due to qubit inhomogeneity through lack of process control become apparent. To benefit from the advanced process control in industry-scale CMOS fabrication facilities, different processing methods will be required. In particular, the double-angle evaporation and lift-off techniques used for current, state-of-the-art superconducting qubits are generally incompatible with modern-day manufacturable processes. Here, we demonstrate a fully CMOS compatible qubit fabrication method, and show results from overlap Josephson junction devices with long coherence and relaxation times, on par with the state-of-the-art. We experimentally verify that Argon milling—the critical step during junction fabrication—and a subtractive-etch process nevertheless result in qubits with average qubit energy relaxation times T 1 reaching 70 µs, with maximum values exceeding 100 µs. Furthermore, we show that our results are still limited by surface losses and not, crucially, by junction losses. The presented fabrication process, therefore, heralds an important milestone towards a manufacturable 300 mm CMOS process for high-coherence superconducting qubits and has the potential to advance the scaling of superconducting device architectures.