gebhart/patrepeval huggingface dataset:
Subpicosecond time-resolved studies of coherent phonon oscillations in thin-film YBa2Cu3O6+x (x&lt;0.4) (1991)

We report the results of the first time-resolved observation of impulsively generated coherent optical phonon oscillations in the semiconducting cuprate compound YBa2Cu3O6+x (x&amp;lt;0.4). The oscillations, which were probed through time-resolved transmissivity modulation, had a period of 237 fs at room temperature, corresponding to a Raman active mode of A1g symmetry at 142 cm−1. No oscillations were observed in the superconducting form of Y-Ba-Cu-O either above or below Tc. The amplitude, frequency, and linewidth of this mode were measured over a temperature range from ∼7 K to room temperature.
On a Chip (2011)

The future of clinical and POC BioMEMS is very bright. With an increasing emphasis on the personalization of medicine and the rising costs of health care, early detection and diagnostics at the POC will be even more important. Early detection implies early intervention, resulting in the saving of lives and reducing overall spending. The potential impact of these technologies on the early diagnosis and management of both communicable and noncommunicable diseases is very high. Many grand challenges applications are possible, e.g., routine tests such as complete blood cell count on a chip that an individual can perform at home; detection of cardiac markers from blood after a perceived heart attack; detection of cancer markers such as exosomes, CTCs from blood, or protein biomarkers in serum; and detection of infectious agents such as virus and bacteria for public health. These applications are expected to result in new diagnostic assays for home, doctor's office, clinical laboratories, and various POC settings.
All-Dielectric Metamaterials Using III–V Semiconductors (2016)

All-dielectric metamaterials consist of arrays of high-index, subwavelength-size Mie resonators that enable manipulation of the electromagnetic permittivity and permeability, but with much lower loss at optical frequencies than their metallic metamaterial counterparts. Most efforts at wavelengths shorter than the mid-infrared, however, have employed silicon, which lacks second-order optical nonlinearities and is not an efficient light emitter. Recently, our group proposed a new class of dielectric metamaterials based upon III–V semiconductors that exhibit strong intrinsic optical nonlinearities and allow for full integration with optoelectronic functionality.
An Approach to Reduce Storage for Homomorphic Computations. (2013)

We introduce a hybrid homomorphic encryption by combining public key encryption (PKE) and somewhat homomorphic encryption (SHE) to reduce storage for most applications of somewhat or fully homomorphic encryption (FHE). In this model, one encrypts messages with a PKE and computes on encrypted data using a SHE or a FHE after homomorphic decryption. To obtain efficient homomorphic decryption, our hybrid schemes is constructed by combining IND-CPA PKE schemes without complicated message paddings with SHE schemes with large integer message space. Furthermore, we remark that if the underlying PKE is multiplicative on a domain closed under addition and multiplication, this scheme has an important advantage that one can evaluate a polynomial of arbitrary degree without recryption. We propose such a scheme by concatenating ElGamal and Goldwasser-Micali scheme over a ring ZN for a composite integer N whose message space is ZN . To be used in practical applications, homomorphic decryption of the base PKE is too expensive. We accelerate the homomorphic evaluation of the decryption by introducing a method to reduce the degree of exponentiation circuit at the cost of additional public keys. Using same technique, we give an efficient solution to the open problem [16] partially. As an independent interest, we obtain another generic conversion method from private key SHE to public key SHE. Differently from Rothblum [23], it is free to choose the message space of SHE.
Iron-deficiency anemia from matriptase-2 inactivation is dependent on the presence of functional Bmp6 (2010)

Hepcidin is the master regulator of iron homeostasis. In the liver, iron-dependent hepcidin activation is regulated through Bmp6 and its membrane receptor hemojuvelin (Hjv), whereas, in response to iron deficiency, hepcidin repression seems to be controlled by a pathway involving the serine protease matriptase-2 (encoded by Tmprss6). To determine the relationship between Bmp6 and matriptase-2 pathways, Tmprss6(-/-) mice (characterized by increased hepcidin levels and anemia) and Bmp6(-/-) mice (exhibiting severe iron overload because of hepcidin deficiency) were intercrossed. We showed that loss of Bmp6 decreased hepcidin levels; increased hepatic iron; and, importantly, corrected hematologic abnormalities in Tmprss6(-/-) mice. This finding suggests that elevated hepcidin levels in patients with familial iron-refractory, iron-deficiency anemia are the result of excess signaling through the Bmp6/Hjv pathway.
BioLPG for Clean Cooking in Sub-Saharan Africa: Present and Future Feasibility of Technologies, Feedstocks, Enabling Conditions and Financing (2021)

Energy supply for clean cooking is a priority for Sub-Saharan Africa (SSA). Liquefied petroleum gas (LPG, i.e., propane or butane or a mixture of both) is an economically efficient, cooking energy solution used by over 2.5 billion people worldwide and scaled up in numerous low- and middle-income countries (LMICs). Investigation of the technical, policy, economic and physical requirements of producing LPG from renewable feedstocks (bioLPG) finds feasibility at scale in Africa. Biogas and syngas from the circular economic repurposing of municipal solid waste and agricultural waste can be used in two groundbreaking new chemical processes (Cool LPG or Integrated Hydropyrolysis and Hydroconversion (IH2)) to selectively produce bioLPG. Evidence about the nature and scale potential of bioLPG presented in this study justifies further investment in the development of bioLPG as a fuel that can make a major contribution toward enabling an SSA green economy and universal energy access. Techno-economic assessments of five potential projects from Ghana, Kenya and Rwanda illustrate what might be possible. BioLPG technology is in the early days of development, so normal technology piloting and de-risking need to be undertaken. However, fully developed bioLPG production could greatly reduce the public and private sector investment required to significantly increase SSA clean cooking capacity.
Cross-Polymerization of Hard Blocks in Segmented Copoly(ether urea)s (2009)

Diacetylene-containing segmented copoly(ether urea) 1 was prepared via a polycondensation of 1,10-diisocyanato-deca-4,6-diyne with bis(3-aminopropyl)poly(tetrahydrofuran) (Mn ≈ 2300 g/mol). The reactive diacetylene spacer, which resides within the hard domains of the segmented elastomer, was cross-polymerized topochemically by means of UV radiation, without disrupting the flexible nature of the material, resulting in an intensely blue insoluble material. The extent of cross-polymerization was determined using solid-state 13C NMR and was found to be ∼10%. The optical properties of the cross-polymerized material could be modified mechanically and thermally as well as by changing the solvent. A study into the mechanochromic behavior—a color change from blue to yellow upon elongation—showed that the color changes are irreversible at strain levels greater than 80%. Polarized UV spectroscopy indicated that upon deformation the polydiacetylene chains orient parallel to the deformation axis. Thermochromic and solvatochromic behavior of 1 was completely irreversible.
Chemical Synergy between Ionophore PBT2 and Zinc Reverses Antibiotic Resistance (2018)

The World Health Organization reports that antibiotic-resistant pathogens represent an imminent global health disaster for the 21st century. Gram-positive superbugs threaten to breach last-line antibiotic treatment, and the pharmaceutical industry antibiotic development pipeline is waning. Here we report the synergy between ionophore-induced physiological stress in Gram-positive bacteria and antibiotic treatment. PBT2 is a safe-for-human-use zinc ionophore that has progressed to phase 2 clinical trials for Alzheimer's and Huntington's disease treatment. In combination with zinc, PBT2 exhibits antibacterial activity and disrupts cellular homeostasis in erythromycin-resistant group A <i>Streptococcus</i> (GAS), methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), and vancomycin-resistant <i>Enterococcus</i> (VRE). We were unable to select for mutants resistant to PBT2-zinc treatment. While ineffective alone against resistant bacteria, several clinically relevant antibiotics act synergistically with PBT2-zinc to enhance killing of these Gram-positive pathogens. These data represent a new paradigm whereby disruption of bacterial metal homeostasis reverses antibiotic-resistant phenotypes in a number of priority human bacterial pathogens.<b>IMPORTANCE</b> The rise of bacterial antibiotic resistance coupled with a reduction in new antibiotic development has placed significant burdens on global health care. Resistant bacterial pathogens such as methicillin-resistant <i>Staphylococcus aureus</i> and vancomycin-resistant <i>Enterococcus</i> are leading causes of community- and hospital-acquired infection and present a significant clinical challenge. These pathogens have acquired resistance to broad classes of antimicrobials. Furthermore, <i>Streptococcus pyogenes</i>, a significant disease agent among Indigenous Australians, has now acquired resistance to several antibiotic classes. With a rise in antibiotic resistance and reduction in new antibiotic discovery, it is imperative to investigate alternative therapeutic regimens that complement the use of current antibiotic treatment strategies. As stated by the WHO Director-General, "On current trends, common diseases may become untreatable. Doctors facing patients will have to say, Sorry, there is nothing I can do for you."
Biomineral Coating Increases Bone Formation by Ex Vivo BMP‐7 Gene Therapy in Rapid Prototyped Poly(l‐lactic acid) (PLLA) and Poly(ε‐caprolactone) (PCL) Porous Scaffolds (2014)

Porousbiodegradable polymer scaffolds are widely utilized for bone tissue engineering, but are not osteoconductive like calcium phosphate scaffolds. We combine indirect solid freeform fabrication (SFF), ex vivo gene therapy, with biomineral coating to compare the effect of biomineral coating on bone regeneration for Poly (L-lactic acid) (PLLA) and Poly (ε-caprolactone) (PCL) scaffolds with the same porous architecture. Scanning electron microscope (SEM) and micro-computed tomography (μ-CT) demonstrate PLLA and PCL scaffolds have the same porous architecture and are completely coated. All scaffolds are seeded with human gingival fibroblasts (HGF) transduced with adenovirus encoded with either bone morphogenetic protein 7 (BMP-7) or green fluorescent protein (GFP), and implanted into mice subcutaneously for 3 and 10 weeks. Only scaffolds with BMP-7 transduced HGFs show mineralized tissue formation. At 3 weeks some blood vessel-like structures are observed in coated PLLA and PCL scaffolds, but there is no significant difference in bone ingrowth between the coated and uncoated scaffolds for either PLLA or PCL. At 10 weeks, however, coated scaffolds (both PLLA and PCL) have significantly more bone ingrowth than uncoated scaffolds, which have more fibrous tissue. Coated PLLA scaffolds have improved mechanical properties compared with uncoated PLLA scaffolds due to increased bone ingrowth.
Expression of MDR‐transporter, ABCB5, in Merkel cell carcinoma (2013)

Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous neuroendocrine neoplasm notoriously refractory to chemotherapy. We have previously found that the multidrug resistance (MDR) transporter, ABCB5, mediates drug resistance in human colonic adenocarcinoma and melanoma where it also defines stem‐like cells responsible for tumor initiation and self‐renewal. The aim of this study was to evaluate the possible role of ABCB5 in MCC. Primary and metastatic MCCs (n=74) were assessed for ABCB5, and mRNA expression and immunoreactivity was confirmed in all cases. Of note, co‐expression of ABCB5 with stem cell markers SOX2 and CD271 was documented in a subset of MCC cells in human tissue, while CD44 and ABCB5 defined separate cell populations. ABCB5 + cells were enriched in patient biopsies after chemotherapy, consistent with relative chemoresistance of this tumor cell subset. In cell line‐derived MCC xenografts in NSG mice, tumors formed by WaGa and MKL‐1 cells demonstrated increased ABCB5 expression after administration of etoposide or carboplatin. In summary, MCCs express ABCB5, and this biomarker may have functional significance regarding both chemoresistance and tumorigenic potential. NIH P50CA93683, Dermatology Foundation Career Development Award and BWH Dermatology new investigator funding.
A New Pressure/Rate Deconvolution Algorithm to Analyze Wireline Formation Tester and Well-Test Data (2009)

Abstract The deconvolved pressure change and its natural-logarithmic time (or Bourdet) derivative are very important for wellbore/reservoir system identification in pressure transient interpretation because they represent the constant-rate drawdown response of the system. In recent years, the use of pressure/rate deconvolution has increased considerably due to significant improvement of the mathematical algorithms. In this paper, we present a robust deconvolution algorithm based on a weighted Euclidean norm in the Tikhonov regularized objective function so that one can assign weights to individual pressure and rate measurement points, and thus define different error estimates for different sections of the data. Incorporating such features into the deconvolution algorithm is very useful to mitigate the effects of unreliable pressure and rate measurements and the sections of the data not obviously consistent with the wellbore/reservoir model. In the deconvolution algorithm, the Levenberg-Marquardt method with a restricted step procedure is used for the minimization of the objective function. We present several applications of the new algorithm using real field pressure/rate transient data sets. In addition to well test data, we apply the algorithm to wireline formation-tester pressure transients which are usually also referred to as Interval Pressure Transient Tests (IPTT). The examples include data with cleanup effects as well as an IPTT test, followed by a conventional Drill Stem Test (DST). To the best of our knowledge, applications of deconvolution to wireline formation-tester pressure transients have been limited to a single publication before. Hence, the deconvolution algorithm and the results in this paper will be useful in designing and interpreting wireline formation tester pressure transients in addition to pressure transient well tests.
Kinetics of polarization reversal in irradiated thin PZT films (2006)

The effect of irradiation with electrons and neutrons and of exposure to synchrotron radiation on cyclic switching of polarization in thin films of lead zirconate titanate Pb(Zr,Ti)O3 (PZT) was studied. It is shown that variations in the shape of switching currents are due to the generation of a spatially nonuniform bound internal field with account for an increase in the rate of bulk screening caused by irradiation. A correlation between structural variations and the evolution of the switching current measured during and after irradiation is established.
ChemInform Abstract: C—H Bond Functionalization via Hydride Transfer: Direct Coupling of Unactivated Alkynes and sp3 C—H Bonds Catalyzed by Platinum Tetraiodide. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Case Report of a Non-small-cell Lung Cancer Patient Who Was EGFR-negative on a Conventional Test but Was Discovered to Have an <i>EGFR</i> Uncommon Mutation on Comprehensive Genomic Profiling and Responded to Afatinib (2020)

背景．次世代シークエンサーを用いた遺伝子パネル検査の登場により，がんゲノム診療が広まっている．今回，従来のEGFR遺伝子変異検査では変異陰性とされていたが，遺伝子パネル検査による再検索でuncommon mutationの存在が判明した症例を経験した．症例．70歳女性．肺腺癌pStage IIIA，左上葉切除後1年で肺内転移により再発した．手術検体を用いたPNA LNA PCR-Clamp法によるEGFR遺伝子変異検査では陰性と報告された．その後7年間にわたり，化学療法・免疫療法を行ったが，progressive diseaseとなった．遺伝子パネル検査（血液および組織）を実施し，EGFR G719DおよびE709Aが検出された．2018年11月からPNA LNA PCR-Clamp法の検索領域が拡大されたため，同法を再検したところ遺伝子パネル検査と同様の変異が検出され，アファチニブを開始し奏効を得た．結論．EGFR遺伝子変異検査の過渡期に変異陰性と診断された非小細胞肺癌症例の中には，治療効果が期待できるuncommon mutationをもつ症例が混在している可能性がある．
Adjuvant-Free Immunization with Hemagglutinin-Fc Fusion Proteins as an Approach to Influenza Vaccines (2010)

The hemagglutinins (HAs) of human H1 and H3 influenza viruses and avian H5 influenza virus were produced as recombinant fusion proteins with the human immunoglobulin Fc domain. Recombinant HA-human immunoglobulin Fc domain (HA-HuFc) proteins were secreted from baculovirus-infected insect cells as glycosylated oligomer HAs of the anticipated molecular mass, agglutinated red blood cells, were purified on protein A, and were used to immunize mice in the absence of adjuvant. Immunogenicity was demonstrated for all subtypes, with the serum samples demonstrating subtype-specific hemagglutination inhibition, epitope specificity similar to that seen with virus infection, and neutralization. HuFc-tagged HAs are potential candidates for gene-to-vaccine approaches to influenza vaccination.
Retrospective cell lineage reconstruction in Humans using short tandem repeats (2017)

Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin 1 . Recently, novel in vivo methods and technologies utilizing genome editing enabled important insights into the cell lineages of animals 2–8 . In contrast, human cell lineage remains restricted to retrospective approaches, which still lack in resolution and cost-efficient solutions. Here we demonstrate a scalable platform for human cell lineage tracing based on Short Tandem Repeats (STRs) targeted by duplex Molecular Inversion Probes (MIPs). With this platform we accurately reproduced a known lineage of DU145 cell lines cells 9 and reconstructed lineages of healthy and metastatic single cells from a melanoma patient. The reconstructed trees matched the anatomical and SNV references while adding further refinements. Our platform allowed to faithfully recapitulate lineages of developmental tissue formation in cells from healthy donors. In summary, our lineage discovery platform can profile informative STR somatic mutations efficiently and we provide a solid, high-resolution lineage reconstruction even in challenging low-mutation-rate healthy single cells.
Human cytomegalovirus protein pp65 mediates accumulation of HLA-DR in lysosomes and destruction of the HLA-DR α-chain (2003)

Human cytomegalovirus (HCMV) has developed multiple strategies to escape immune recognition. Here, we demonstrate that HCMV down-regulates HLA-DR expression in infected interferon gamma (IFN-gamma)-stimulated fibroblasts at 1 day after infection. Decreased HLA-DR expression was not observed on cells infected with an HCMV strain lacking the pp65 gene (RVAD65), but was observed on cells transfected with the pp65 gene. HLA-DR expression accumulated in vacuoles near the nucleus in HCMV-infected, but not in uninfected or RVAD65-infected cells. In addition, the HLA-DR alpha-chain, but not the beta-chain or HLA-DM, was degraded in HCMV-infected but not in RVAD65-infected cells. Thus, the HCMV protein pp65 mediates decreased expression of HLA-DR, by mediating an accumulation of HLA class II molecules in lysosomes that results in degradation of the HLA-DR alpha-chain.
On capacity achieving property of rotational coding for acyclic deterministic wireless networks (2010)

Abstract—It has been shown that the well-known cutset bounds can be achieved for deterministic wireless networks by performing random coding at each intermediate node. The complexity and forwarding overhead of random coding scheme prohibits its application in practice. Recently, a practical low complexity alternative, rotational coding scheme, was proposed in [1] where it was proved that the rotational coding can achieve the capacity of the layered deterministic wireless networks. In this paper, we extend the result and prove that the rotational coding is in fact capacity achieving for a general acyclic network. Our result adds to the practical property of rotational coding scheme and makes it desirable for communication networks with arbitrary topology as long as there is no directional cycle in the network. I.
From the EiC: The IEEE Radar Journal is Born (2023)

Formally launched in October 2022, IEEE Transactions on Radar Systems (TRS) has now “gestated” for nine months, making it a good time to report to the radar community on how this new journal is progressing. Let’s begin with some pertinent metrics. As of this writing, 30 papers have been accepted for publication, with a final decision acceptance rate of 32%. In addition, more than 150 papers have thus far been submitted, indicating a strong demand signal by the global radar community for a dedicated IEEE journal. Moreover, we have just been notified that TRS has been deemed a “High Performer” by ranking in the first quartile of IEEE transactions/journals in terms of both <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">average time to first decision</i> and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">average time to online posting</i> . In short, TRS is performing quite well.
The TolTEC camera: polarimetric commissioning and performance of the continuously rotating half-wave plate (2022)

An ambient-temperature Continuously Rotating Half-Wave Plate (CRHWP) modulates the input polarization signal thereby enabling removal of low-frequency (1/f) noise from polarized flux measurements. This 1/f noise arises from atmospheric turbulence as well as from effects intrinsic to certain detectors. Here, we describe the design and performance of the half wave plate rotator and achromatic half-wave plate for the the new imaging polarimeter, TolTEC. These components are mounted in front of the cryostat window and operate at ambient temperature. The Half-Wave Plate Rotator (HWPR) spins the half-wave plate at 2 revolutions per second. The rotation mechanism consists of nine air bearings to provide low-friction motion and a frameless torque motor to directly drive rotation. The orientation of the rotor and half-wave plate are recorded using a high-precision optical encoder. We review the experimental requirements and technical design of the rotator as well as the associated electronics, pneumatics, and software.
Prediction of the skull overheating during high intensity focused ultrasound transcranial brain therapy (2005)

Ultrasound brain therapy is currently limited by the strong phase and amplitude aberrations induced by the heterogeneities of the skull. However, the development of aberration correction techniques has made it possible to correct the beam distortion induced by the skull and to produce a sharp focus in the brain. Moreover, using the density of the skull bone that can be obtained with high-resolution CT scans, the corrections needed to produced this sharp focus can be calculated using ultrasound propagation models. We propose a model for computing the temperature elevation in the skull during high intensity focused ultrasound (HIFU) transcranial therapy. Based on CT scans, the wave propagation through the skull is computed with 3D finite difference wave propagation software. The acoustic simulation is combined with a 3D thermal diffusion code and the temperature elevation inside the skull is computed. Finally, the simulation is validated experimentally by measuring the temperature elevation in several locations of the skull.