gebhart/patrepeval huggingface dataset:
Fabrication of Fully Solution Processed Inorganic Nanocrystal Photovoltaic Devices (2016)

We demonstrate a method for the preparation of fully solution processed inorganic solar cells from a spin and spray coating deposition of nanocrystal inks. For the photoactive absorber layer, colloidal CdTe and CdSe nanocrystals (3-5 nm) are synthesized using an inert hot injection technique and cleaned with precipitations to remove excess starting reagents. Similarly, gold nanocrystals (3-5 nm) are synthesized under ambient conditions and dissolved in organic solvents. In addition, precursor solutions for transparent conductive indium tin oxide (ITO) films are prepared from solutions of indium and tin salts paired with a reactive oxidizer. Layer-by-layer, these solutions are deposited onto a glass substrate following annealing (200-400 °C) to build the nanocrystal solar cell (glass/ITO/CdSe/CdTe/Au). Pre-annealing ligand exchange is required for CdSe and CdTe nanocrystals where films are dipped in NH4Cl:methanol to replace long-chain native ligands with small inorganic Cl- anions. NH4Cl(s) was found to act as a catalyst for the sintering reaction (as a non-toxic alternative to the conventional CdCl2(s) treatment) leading to grain growth (136±39 nm) during heating. The thickness and roughness of the prepared films are characterized with SEM and optical profilometry. FTIR is used to determine the degree of ligand exchange prior to sintering, and XRD is used to verify the crystallinity and phase of each material. UV/Vis spectra show high visible light transmission through the ITO layer and a red shift in the absorbance of the cadmium chalcogenide nanocrystals after thermal annealing. Current-voltage curves of completed devices are measured under simulated one sun illumination. Small differences in deposition techniques and reagents employed during ligand exchange have been shown to have a profound influence on the device properties. Here, we examine the effects of chemical (sintering and ligand exchange agents) and physical treatments (solution concentration, spray-pressure, annealing time and annealing temperature) on photovoltaic device performance.
The proton to electron stoichiometry of steady-state photosynthesis in living plants: A proton-pumping Q cycle is continuously engaged (2000)

A noninvasive technique is introduced with which relative proton to electron stoichiometries (H(+)/e(-) ratios) for photosynthetic electron transfer can be obtained from leaves of living plants under steady-state illumination. Both electron and proton transfer fluxes were estimated by a modification of our previously reported dark-interval relaxation kinetics (DIRK) analysis, in which processes that occur upon rapid shuttering of the actinic light are analyzed. Rates of turnover of linear electron transfer through the cytochrome (cyt) b(6)f complex were estimated by measuring the DIRK signals associated with reduction of cyt f and P(700). The rates of proton pumping through the electron transfer chain and the CF(O)-CF(1) ATP synthase (ATPase) were estimated by measuring the DIRK signals associated with the electrochromic shifting of pigments in the light-harvesting complexes. Electron transfer fluxes were also estimated by analysis of saturation pulse-induced changes in chlorophyll a fluorescence yield. It was shown that the H(+)/e(-) ratio, with respect to both cyt b(6)f complex and photosystem (PS) II turnover, was constant under low to saturating illumination in intact tobacco leaves. Because a H(+)/e(-) ratio of 3 at a low light is generally accepted, we infer that this ratio is maintained under conditions of normal (unstressed) photosynthesis, implying a continuously engaged, proton-pumping Q cycle at the cyt b(6)f complex.
Granular crystals: Nonlinear dynamics meets materials engineering (2015)

The freedom to choose the size, stiffness, and spatial distribution of macroscopic particles in a lattice makes granular crystals easily tailored building blocks for shock-absorbing materials, sound-focusing devices, acoustic switches, and other exotica.
CoFe-Coated Carbon Nanotube Probes for Magnetic Force Microscope (2005)

CoFe-coated carbon nanotube (CNT) probes have been successfully fabricated by a radio-frequency sputtering method. The sputtering conditions for obtaining a uniform ferromagnetic film on the CNT probe were investigated. The optimal sputtering conditions were determined from the observations using a scanning electron microscope and an atomic force microscope. CNT magnetic force microscope (MFM) probes prepared under optimized conditions provided us clear images with an ultimate lateral resolution of approximately 10 nm.
New aluminum oxide single crystals for volumetric optical data storage (2003)

Spectroscopic properties of new aluminum oxide crystals for volumetric optical data storage were investigated. Magnesium impurity and double oxygen vacancy defects are responsible for the main optical properties of the new material.
Molecular beam epitaxial growth of monolithic 1.55 μm vertical cavity surface emitting lasers with AlGaAsSb/AlAsSb Bragg mirrors (2000)

The molecular beam epitaxy and the characterization of single-step grown long wavelength vertical cavity surface emitting lasers (LW–VCSEL) are reported. The devices were fabricated using highly reflective AlGaAsSb/AlAsSb distributed Bragg reflectors (DBRs), and an AlGaInAs-based active region embedding a tunnel (or Esaki) junction. The VCSELs operate at 1.55 μm at room temperature with a threshold current density of 1.4 kA/cm2. Characterization of the VCSELs and DBRs’ thermal and electrical properties is presented. Major improvement on the voltage drop in an InGaAs capped DBR is demonstrated, resulting in a value as low as 40 mV/pair.
Lateral Flow Aptasensor for Small Molecule Targets Exploiting Adsorption and Desorption Interactions on Gold Nanoparticles (2017)

A lateral flow assay (LFA) can provide a rapid and cost-effective means to detect targets in situ; however, existing LFA formats (predominantly sandwich assays) are not suitable for small molecule targets. We present a new LFA design that probes the dissociation of aptamers from the surface of gold nanoparticles upon recognition of small targets. The target-induced removal of aptamer molecules from the surface of the colored particles results in the particles being captured on a test line comprised of the protein bovine serum albumin immobilized on nitrocellulose. On the other hand, in the absence of target, aptamer coated particles are protected from capture on the test line and are instead captured at a control line comprised of the protein lysozyme. This protein is strongly positively charged under measurement conditions and therefore captures all gold nanoparticles regardless of the presence of aptamers. The effectiveness and operation mechanism of this simply fabricated sensor was demonstrated by using a previously reported 35-mer aptamer for a small molecule, 17β-estradiol. The sensor exhibited nanomolar level of detection, excellent selectivity against potential interfering molecules, and robust operation in natural river water samples. The simplicity and performance of the sensor platform renders it applicable to a wide range of other aptamers targeting small molecules, as we demonstrated with a novel bisphenol A aptamer. Additionally, we show that our LFA design is not confined to the specific proteins used as test and control lines, provided that their charge is appropriate to modulate the interaction with aptamer-coated or bare nanoparticles.
High-Rate, Ultralong Cycle-Life Lithium/Sulfur Batteries Enabled by Nitrogen-Doped Graphene (2014)

Nitrogen-doped graphene (NG) is a promising conductive matrix material for fabricating high-performance Li/S batteries. Here we report a simple, low-cost, and scalable method to prepare an additive-free nanocomposite cathode in which sulfur nanoparticles are wrapped inside the NG sheets (S@NG). We show that the Li/S@NG can deliver high specific discharge capacities at high rates, that is, ∼ 1167 mAh g(-1) at 0.2 C, ∼ 1058 mAh g(-1) at 0.5 C, ∼ 971 mAh g(-1) at 1 C, ∼ 802 mAh g(-1) at 2 C, and ∼ 606 mAh g(-1) at 5 C. The cells also demonstrate an ultralong cycle life exceeding 2000 cycles and an extremely low capacity-decay rate (0.028% per cycle), which is among the best performance demonstrated so far for Li/S cells. Furthermore, the S@NG cathode can be cycled with an excellent Coulombic efficiency of above 97% after 2000 cycles. With a high active S content (60%) in the total electrode weight, the S@NG cathode could provide a specific energy that is competitive to the state-of-the-art Li-ion cells even after 2000 cycles. The X-ray spectroscopic analysis and ab initio calculation results indicate that the excellent performance can be attributed to the well-restored C-C lattice and the unique lithium polysulfide binding capability of the N functional groups in the NG sheets. The results indicate that the S@NG nanocomposite based Li/S cells have a great potential to replace the current Li-ion batteries.
Prospect of Nickel-based Superalloys with Low Cr and High Re Contents. (2002)

There is a clear trend of lowering Cr and increasing Re content in the evolution from the 1st-to the 2nd-and to the 3rd-generation Ni-based single crystal (SC) superalloys. Following this trend, two groups of superalloys were made with the aid of the d-electrons concept. One is the A-group which is characterized by the lower Cr and the higher Re contents in the alloys than in the 3rd-generation SC alloys. A homogeneous microstructure was obtained in these A-group superalloys containing 0, 1 and 2 mass% Cr, while their Re and Co contents were set at about 8.5 mass% and 13.5 mass% respectively. The other is the B-group which is characterized by the lower Re content than the A-group. Three alloys in the B-group containing 2.5, 4.2 and 12.1 mass% Cr were studied for the comparison with the A-group. According to a hot corrosion test, weight gain occurred in a Cr-free alloy instead of observing weight loss in Cr containing alloys. Hot corrosion resistance of 2 mass% Cr alloy was quite good as long as the alloy contains about 8.5 mass% Re. The oxidation resistance was improved remarkably in 1 mass% Cr alloy than in the Cr-free alloy. It was found that the addition of at least 2 mass% Cr into superalloys is necessary in order to keep good surface stability at high temperatures. Also, it was seen that Re is a harmful element for oxidation resistance.
A new machine learning approach for predicting likelihood of recurrence following ablation for atrial fibrillation from CT (2021)

Abstract Objective To investigate left atrial shape differences on CT scans of atrial fibrillation (AF) patients with (AF+) versus without (AF−) post-ablation recurrence and whether these shape differences predict AF recurrence. Methods This retrospective study included 68 AF patients who had pre-catheter ablation cardiac CT scans with contrast. AF recurrence was defined at 1 year, excluding a 3-month post-ablation blanking period. After creating atlases of atrial models from segmented AF+ and AF− CT images, an atlas-based implicit shape differentiation method was used to identify surface of interest (SOI). After registering the SOI to each patient model, statistics of the deformation on the SOI were used to create shape descriptors. The performance in predicting AF recurrence using shape features at and outside the SOI and eight clinical factors (age, sex, left atrial volume, left ventricular ejection fraction, body mass index, sinus rhythm, and AF type [persistent vs paroxysmal], catheter-ablation type [Cryoablation vs Irrigated RF]) were compared using 100 runs of fivefold cross validation. Results Differences in atrial shape were found surrounding the pulmonary vein ostia and the base of the left atrial appendage. In the prediction of AF recurrence, the area under the receiver-operating characteristics curve (AUC) was 0.67 for shape features from the SOI, 0.58 for shape features outside the SOI, 0.71 for the clinical parameters, and 0.78 combining shape and clinical features. Conclusion Differences in left atrial shape were identified between AF recurrent and non-recurrent patients using pre-procedure CT scans. New radiomic features corresponding to the differences in shape were found to predict post-ablation AF recurrence.
Cross‐validation of magnetic resonance elastography and ultrasound‐based transient elastography: A preliminary phantom study (2009)

These two noninvasive methods, MRE and UTE, provide clinicians with important new options for improving patient care regarding liver diseases in terms of the diagnosis, prognosis, and monitoring of fibrosis progression, as well for evaluating the efficacy of treatment.
DLC‐1, a Rho GTPase‐activating protein with tumor suppressor function, is essential for embryonic development (2005)

DLC-1 (deleted in liver cancer 1) is a Rho GTPase-activating protein that is able to inhibit cell growth and suppress tumorigenesis. We have used homologous recombination to inactivate the mouse DLC-1 gene (Arhgap7). Mice heterozygous for the targeted allele were phenotypically normal, but homozygous mutant embryos did not survive beyond 10.5 days post coitum. Histological analysis revealed that DLC-1-/- embryos had defects in the neural tube, brain, heart, and placenta. Cultured fibroblasts from DLC-1-deficient embryos displayed alterations in the organization of actin filaments and focal adhesions.
Novel copper(I) complexes and their chemistry relative to the oxidative-coupling of 2,6-xylenol (1987)

Epithelial tissues mechanically deform the surrounding extracellular matrix during embryonic development, wound repair, and tumor invasion. Ex vivo measurements of such multicellular tractions within three-dimensional (3D) biomaterials could elucidate collective dissemination during disease progression and enable preclinical testing of targeted antimigration therapies. However, past 3D traction measurements have been low throughput due to the challenges of imaging and analyzing information-rich 3D material deformations. Here, we demonstrate a method to profile multicellular clusters in a 96-well-plate format based on spatially heterogeneous contractile, protrusive, and circumferential tractions. As a case study, we profile multicellular clusters across varying states of the epithelial-mesenchymal transition, revealing a successive loss of protrusive and circumferential tractions, as well as the formation of localized contractile tractions with elongated cluster morphologies. These cluster phenotypes were biochemically perturbed by using drugs, biasing toward traction signatures of different epithelial or mesenchymal states. This higher-throughput analysis is promising to systematically interrogate and perturb aberrant mechanobiology, which could be utilized with human-patient samples to guide personalized therapies.
Structure and formation mechanism of interface-modified layer in ramp-edge Josephson junctions with la-doped 123-type superconducting electrodes (2003)

Ramp-edge-type Josephson junctions (JJ) with interface-modified barriers were fabricated. Yb/sub 0.9/La/sub 0.2/Ba/sub 1.9/Cu/sub 3/O/sub y/ and Y/sub 0.9/La/sub 0.2/Ba/sub 1.9/Cu/sub 3/O/sub y/ were used for the counter- and base-electrodes, respectively. Reliable junctions with I/sub c//spl sime/1 mA and 1/spl sigma/=6.5-8.0% for 25-100 JJ arrays were reproducibly obtained. For the junctions, the structure and composition of the barrier were investigated using a transmission electron microscope. A rather homogeneous layer with a thickness of a few nm was observed in the barrier region. The layer had a cubic lattice with a/spl sime/0.39/spl times/0.40 nm/sup 2/ and its cationic composition was Ba:La:(Y+Yb):Cu=38:10:20:32. It implies that the barrier consists of a thin layer of a cubic perovskite (Ba,La)(Y,Yb,Cu)O/sub 3/. The existence of La seems to stabilize the cubic perovskite and improve homogeneity of the barrier layer.
Design of a Novel Two Degree-of-Freedom Ankle-Foot Orthosis (2006)

An ankle-foot orthosis (AFO) is commonly used to help subjects with weakness of ankle dorsiflexor muscles due to peripheral or central nervous system disorders. Both these disorders are due to the weakness of the tibialis anterior muscle, which results in the lack of dorsiflexion assist moment. The deformity and muscle, weakness of one joint in the lower extremity influences the stability of the adjacent joints, thereby requiring compensatory adaptations. We present an innovative ankle-foot orthosis (AFO). The prototype AFO would introduce greater functionality over currently marketed devices by means of its pronation-supination degree of freedom in addition to flexion/extension. This orthosis can be used to measure joint forces and moments applied by the human at both joints. In the future, by incorporation of actuators in the device, it will be used as a training device to restore a normal walking pattern.
Efficient Shared Peak Counting in Database Peptide Search Using Compact Data Structure for Fragment-Ion Index (2019)

Database search is the most commonly employed method for identification of peptides from MS/MS spectra data. The search involves comparing experimentally obtained MS/MS spectra against a set of theoretical spectra predicted from a protein sequence database. One of the most commonly employed similarity metrics for spectral comparison is the shared-peak count between a pair of MS/MS spectra. Most modern methods index all generated fragment-ion data from theoretical spectra to speed up the shared peak count computations between a given experimental spectrum and all theoretical spectra. However, the bottleneck for this method is the gigantic memory footprint of fragment-ion index that leads to non-scalable solutions. In this paper, we present a novel data structure, called Compact Fragment-Ion Index Representation (CFIR), that efficiently compresses highly redundant ion-mass information in the data to reduce the index size. Our proposed data structure outperforms all existing fragment-ion indexing data structures by at least 2× in memory consumption while exhibiting the same time complexity for index construction and peptide search. The results also show comparable indexing speed, search speed and speedup scalability for CFIR-index and the state-of-the-art algorithms.
Immune reconstitution Immune reconstitution following allogeneic stem cell transplantation in recipients conditioned by low intensity vs myeloablative regimen (2001)

Summary: We have investigated the immune status of patients with hematologic malignancies treated with a low intensity conditioning in preparation for allogeneic stem cell transplantation. Conditioning consisted of fludarabine, anti-T lymphocyte globulin and low-dose busulfan, followed by infusion of allogeneic blood stem cells. This protocol resulted in rapid engraftment and complete replacement of host with donor hematopoietic cells. Immunological parameters of these patients were compared to those patients who were conditioned by an aggressive myeloablative regimen. Distribution of cell surface markers of lymphocyte subsets from both groups of patients was similar, but different from that of normal control cells. Reduced intensity or non-myeloablative conditioning prior to allogeneic stem cell transplantation (NST), hardly lowered the normal T cell-dependent mitogenic response even during the early period following transplant, while the myeloablative treatments resulted in a suppressed mitogenic reaction and in slow immune recovery. Reactivity of non-MHC restricted cytotoxic T cells was also at a normal level in patients who were treated with NST. We conclude that stem cell engraftment following reduced conditioning may result in early reconstitution of immune responses assessed in vitro. We hypothesize that clinical application of NST may lead to faster development of effective immune responses against residual host-type malignant and abnormal non-malignant hematopoietic cells, although the role of fludarabine on post-transplant infections remains to be investigated in a larger cohort of patients. Bone Marrow Transplantation (2001) 28, 243–249.
SCIDIVE: a stateful and cross protocol intrusion detection architecture for voice-over-IP environments (2004)

Voice-over-IP (VoIP) systems are gaining in popularity as the technology for transmitting voice traffic over IP networks. As the popularity of VoIP systems increases, they are being subjected to different kinds of intrusions some of which are specific to such systems and some of which follow a general pattern. VoIP systems pose several new challenges to intrusion detection system (IDS) designers. First, these systems employ multiple protocols for call management (e.g., SIP) and data delivery (e.g., RTP). Second, the systems are distributed in nature and employ distributed clients, servers and proxies. Third, the attacks to such systems span a large class, from denial of service to billing fraud attacks. Finally, the systems are heterogeneous and typically under several different administrative domains. In this paper, we propose the design of an intrusion detection system targeted to VoIP systems, called SCIDIVE (pronounced "Skydive"). SCIDIVE is structured to detect different classes of intrusions, including, masquerading, denial of service, and media stream-based attacks. It can operate with both classes of protocols that compose VoIP systems - call management protocols (CMP), e.g., SIP, and media delivery protocols (MDP), e.g., RTP. SCIDIVE proposes two abstractions for VoIP IDS - stateful detection and cross-protocol detection. Stateful detection denotes assembling state from multiple packets and using the aggregated state in the rule-matching engine. Cross protocol detection denotes matching rules that span multiple protocols. SCIDIVE is demonstrated on a sample VoIP system that comprises SIP clients and SIP proxy servers with RTP as the data delivery protocol. Four attack scenarios are created and the accuracy and the efficiency of the system evaluated with rules meant to catch these attacks.
Biodegradable nanoparticle delivery of inactivated swine influenza virus vaccine provides heterologous cell-mediated immune response in pigs (2017)

Abstract Swine influenza virus (SwIV) causes considerable economic loss to pig industry, and some SwIV are zoonotic. This study was conducted to evaluate the cross-protective efficacy of PLGA (poly lactic-co-glycolic acid) nanoparticles (NPs) encapsulated SwIV vaccine in pigs. Killed SwIV H1N2 (δ lineage) antigens (KAg) were encapsulated in PLGA NPs of 200–300 nm (PLGA-KAg NPs), and influenza antibody-free pigs were prime-boost vaccinated intranasally as mist and challenged using a heterologous, virulent and zoonotic SwIV H1N1 (γ lineage). PLGA-KAg NPs induced maturation of pig macrophages and dendritic cells in vitro. In vaccinated pigs, PLGA-KAg NPs induced antigen specific lymphocyte proliferation and enhanced the frequency of T-helper/memory cells and cytotoxic T cells in peripheral blood mononuclear cells (PBMCs). In virus challenged pigs, the PLGA-KAg NPs vaccine rescued virus induced clinical fever, reduced the gross lung pathology, reduced the virus load in the lung sections with complete clearance of the virus from the lungs of most of the pigs; but the nasal virus shedding was not reduced. Immunologically, at post-challenge day 6 in a recall response in PBMCs of PLGA KAg NPs vaccinated pigs, a significant increase in IFN-γ secreting T cells against both vaccine and challenge viruses were detected. However, humoral immune response in those pigs was not augmented. In conclusion, intranasal delivery of PLGA NPs based SwIV induced cross-protective response through specific cell-mediated response. Future studies are aimed at boosting the mucosal antibody response.