gebhart/patrepeval huggingface dataset:
Transfer Learning Using Ensemble Neural Networks for Organic Solar Cell Screening (2019)

Organic Solar Cells are a promising technology for solving the clean energy crisis in the world. However, generating candidate chemical compounds for solar cells is a time-consuming process requiring thousands of hours of laboratory analysis. For a solar cell, the most important property is the power conversion efficiency which is dependent on the highest occupied molecular orbitals (HOMO) values of the donor molecules. Recently, machine learning techniques have proved to be very useful in building predictive models for HOMO values of donor structures of Organic Photovoltaic Cells (OPVs). Since experimental datasets are limited in size, current machine learning models are trained on data derived from calculations based on density functional theory (DFT). Molecular line notations such as SMILES or InChI are popular input representations for describing the molecular structure of donor molecules. The two types of line representations encode different information, such as SMILES defines the bond types while InChi defines protonation. In this work, we present an ensemble deep neural network architecture, called SINet, which harnesses both the SMILES and InChI molecular representations to predict HOMO values and leverage the potential of transfer learning from a sizeable DFT-computed dataset- Harvard CEP to build more robust predictive models for relatively smaller HOPV datasets. Harvard CEP dataset contains molecular structures and properties for 2.3 million candidate donor structures for OPV while HOPV contains DFT-computed and experimental values of 350 and 243 molecules respectively. Our results demonstrate significant performance improvement from the use of transfer learning and leveraging both molecular representations.
Establishing life is a calcium-dependent TRiP: Transient receptor potential channels in reproduction (2018)

Calcium plays a key role in many different steps of the reproduction process, from germ cell maturation to placental development. However, the exact function and regulation of calcium throughout subsequent reproductive events remains rather enigmatic. Successful pregnancy requires the establishment of a complex dialogue between the implanting embryo and the endometrium. On the one hand, endometrial cell will undergo massive changes to support an implanting embryo, including stromal cell decidualization. On the other hand, trophoblast cells from the trophectoderm surrounding the inner cell mass will differentiate and acquire new functions such as hormone secretion, invasion and migration. The need for calcium in the different gestational processes implicates the presence of specialized ion channels to regulate calcium homeostasis. The superfamily of transient receptor potential (TRP) channels is a class of calcium permeable ion channels that is involved in the transformation of extracellular stimuli into the influx of calcium, inducing and coordinating underlying signaling pathways. Although the necessity of calcium throughout reproduction cannot be negated, the expression and functionality of TRP channels throughout gestation remains elusive. This review provides an overview of the current evidence regarding the expression and function of TRP channels in reproduction.
Human cell-derived tissue-engineered heart valve with integrated Valsalva sinuses: towards native-like transcatheter pulmonary valve replacements (2019)

Transcatheter valve replacement indication is currently being extended to younger and lower-risk patients. However, transcatheter prostheses are still based on glutaraldehyde-fixed xenogeneic materials. Hence, they are prone to calcification and long-term structural degeneration, which are particularly accelerated in younger patients. Tissue-engineered heart valves based on decellularized in vitro grown tissue-engineered matrices (TEM) have been suggested as a valid alternative to currently used bioprostheses, showing good performance and remodeling capacity as transcatheter pulmonary valve replacement (TPVR) in sheep. Here, we first describe the in vitro development of human cell-derived TEM (hTEM) and their application as tissue-engineered sinus valves (hTESVs), endowed with Valsalva sinuses for TPVR. The hTEM and hTESVs were systematically characterized in vitro by histology, immunofluorescence, and biochemical analyses, before they were evaluated in a pulse duplicator system under physiological pulmonary pressure conditions. Thereafter, transapical delivery of hTESVs was tested for feasibility and safety in a translational sheep model, achieving good valve performance and early cellular infiltration. This study demonstrates the principal feasibility of clinically relevant hTEM to manufacture hTESVs for TPVR.
Self-aligning silicon groove technology platform for the low cost optical module (2003)

The SASGT (Self-Aligning Silicon Groove Technology) platform has been developed for use as a real passive alignment. Key technologies of this platform are precise size control technology for optical active chips, three-step anisotropic etching technology for the silicon optical bench, and flux-and pressure-free die bonding technology. Precisely size controlled laser diode chip was fabricated by etching of V-grooves for cleaving along the [110] and [110] directions. We obtained the size controlled laser chips, which have a width of 298 /spl mu/m and an active stripe in the center with the accuracy of /spl plusmn/0.5 /spl mu/m, respectively. The silicon groove for positioning of laser diode, formed by three-step etching, has a width of 298 /spl mu/m and a depth of 25 /spl mu/m. By carefully controlling the orientation of the silicon wafer and the chemical etching environment, the size accuracy of laser diode site can be better than /spl plusmn/0.5 um. In addition, the flux and pressure-free bonding of laser diode chips on silicon groove was successfully accomplished by using the surface treated Au-Sn solder under the evacuated nitrogen gas flowing furnace. We achieved accurate positioning of the optical components without any auxiliary tools such as high resolution bonder, alignment mark, solder bump and guide shell. By using the SASGT platform, the coupling efficiency of the laser diode module was achieved of better than 8% and the responsivity of the photo diode module was estimated to be better than 0.85 A/W.
Mechanical and morphometric study of mitral valve chordae tendineae and related papillary muscle (2020)

The mitral valve (MV) apparatus is a complex mechanical structure including annulus, valve leaflets, papillary muscles (PMs) and connected chordae tendineae. Chordae anchor to the papillary muscles to help the valve open and close properly during one cardiac cycle. It is of paramount importance to understand the functional, mechanical, and microstructural properties of mitral valve chordae and connecting PMs. In particular, little is known about the biomechanical properties of the anterior and posterior papillary muscle and corresponding chords. In this work, we performed uniaxial and biaxial tensile tests on the anterolateral (APM) and posteromedial papillary muscle (PPM), and their respective corresponding chordae tendineae, chordae<sup>APM</sup> and chordae<sup>PPM</sup>, in porcine hearts. Histology was carried out to link the microstructure and macro-mechanical behavior of the chordae and PMs. Our results demonstrate that chordae<sup>PPM</sup> are less in number, but significantly longer and stiffer than chordae<sup>APM</sup>. These different biomechanical properties may be partially explained by the higher collagen core ratio and larger collagen fibril density of chordae<sup>PPM</sup><sub>.</sub> No significant mechanical or microstructural differences were observed along the circumferential and longitudinal directions of APM and PPM samples. Data measured on chordae and PMs were further fitted with the Ogden and reduced Holzapfel - Ogden strain energy functions, respectively. This study presents the first comparative anatomical, mechanical, and structural dataset of porcine mitral valve chordae and related PMs. Results indicate that a PM based classification of chordae will need to be considered in the analysis of the MV function or planning a surgical treatment, which will also help developing more precise computational models of MV.
Hydrostatic pore water pressure revisited (2022)

Abstract Hydrostatic or “normal” pressure can be easily visualized as a water column with pressure given by ρgh and any departures classified as abnormal pressure. This is the basis for commonly used hydrostatic pressure depth trends in sedimentary basins that are constructed on assumptions of constant gradients and are datumed at mean sea level or ground level. But the straightforward water column concept does not upscale in a simple way to sedimentary basins where the zones of interest are several thousands of metres below the land or sea surface. Sedimentary basins are heterogeneous, including stacked, confined reservoirs and variations in pore water composition. It is possible to construct pressure‐depth profiles that honour the geology and hydrostratigraphy of a basin and these give different hydrostatic baselines from simple constant gradients hung from familiar local datums such as ground level. Key steps are using a reservoir‐specific datums such as the water table or potentiometric surface relevant to that unit, then building a pressure‐depth trend that represents the pore fluid salinity variation and density profile throughout the reservoir unit. At a given depth, this version of hydrostatic may predict pressures several hundred psi different from a single density gradient hung from a datum local to the well, and exhibit a notched profile reflecting the geological and hydrological stratigraphy. This construct redefines normal and abnormal pore fluid pressures in sedimentary basins. The impacts of this alternative approach to sedimentary basin hydrostatics, even if data are limited and pressure profiles have to be framed probabilistically, extend to many aspects of studying and interacting with fluid systems in sedimentary basins including basin modelling, petroleum systems analysis, well planning and well operations.
Investigating the electronic properties of Al2O3/Cu(In,Ga)Se2 interface (2015)

Atomic layer deposited (ALD) Al2O3 films on Cu(In,Ga)Se2 (CIGS) surfaces have been demonstrated to exhibit excellent surface passivation properties, which is advantageous in reducing recombination losses at the rear metal contact of CIGS thin-film solar cells. Here, we report, for the first time, experimentally extracted electronic parameters, i.e. fixed charge density (Qf) and interface-trap charge density (Dit), for as-deposited (AD) and post-deposition annealed (PDA) ALD Al2O3 films on CIGS surfaces using capacitance–voltage (C-V) and conductance-frequency (G-f) measurements. These results indicate that the AD films exhibit positive fixed charges Qf (approximately 1012 cm−2), whereas the PDA films exhibit a very high density of negative fixed charges Qf (approximately 1013 cm−2). The extracted Dit values, which reflect the extent of chemical passivation, were found to be in a similar range of order (approximately 1012 cm−2 eV−1) for both AD and PDA samples. The high density of negative Qf in the bulk of the PDA Al2O3 film exerts a strong Coulomb repulsive force on the underlying CIGS minority carriers (ns), preventing them to recombine at the CIGS/Al2O3 interface. Using experimentally extracted Qf and Dit values, SCAPS simulation results showed that the surface concentration of minority carriers (ns) in the PDA films was approximately eight-orders of magnitude lower than in the AD films. The electrical characterization and estimations presented in this letter construct a comprehensive picture of the interfacial physics involved at the Al2O3/CIGS interface.
Enantioselective Recognition between Polydiacetylene Nucleolipid Monolayers and Complementary Oligonucleotides (2010)

A two-dimensional bio/synthetic hybrid system at the air-solution interface made of a polymerized diacetylene Langmuir film with nucleobase modified headgroups is presented. The polymerized film presents a crystalline array of nucleobases, capable of specific binding of complementary mononucleoside or oligonucleotide sequences. Mixed monolayers of the linear polyconjugated polydiacetylene (PDA) films derivatized with cytosine (10,12-pentacosadiyne-cytidyl, PDC) monomers and alcohol-terminated diacetylene lipid (10,12-pentacosadiynol, PDOH) at a 3:1 ratio (PDC 75%) were compressed and polymerized at the air-water interface with circular polarized light (CPL) or nonpolarized UV light. Here we report a grazing incidence X-ray diffraction (GIXD) investigation of PDC films polymerized to different chirality and hybridized with complementary ssDNA strands. We have demonstrated enantioselective interactions on synthetic structured interfaces produced by Langmuir surface compression followed by polymerization with circular polarized UV light (CPL). The left- and right-CPL polymerized light exhibit the same well-defined crystalline structure. The observed difference between left- and right-CPL polymerized PDC 75% Langmuir films compressed over the complementary mononucleotide guanosine or hybridized with fully complementary ssG(12)T(5) oligonucleotide in the subphase suggests that they are indeed enantiomeric structures, capable of enantioselective binding of their natural ligand, guanosine, solely as a result of surface induced asymmetry in "left" but not in "right" form. This observation may also be related to the intriguing question of chiral selection during the early period of "Origin of Life". We show that achiral compounds, as a result of irradiation with circular polarized light, can organize in chiral surface structures capable of amplification of biopolymer binding of particular handedness.
Entropy-Based Semi-Fragile Watermarking of Remote Sensing Images in the Wavelet Domain (2019)

This article presents a semi-fragile image tampering detection method for multi-band images. In the proposed scheme, a mark is embedded into remote sensing images, which have multiple frequential values for each pixel, applying tree-structured vector quantization. The mark is not embedded into each frequency band separately, but all the spectral values (known as signature) are used. The mark is embedded in the signature as a means to detect if the original image has been forged. The image is partitioned into three-dimensional blocks with varying sizes. The size of these blocks and the embedded mark is determined by the entropy of each region. The image blocks contain areas that have similar pixel values and represent smooth regions in multispectral or hyperspectral images. Each block is first transformed using the discrete wavelet transform. Then, a tree-structured vector quantizer (TSVQ) is constructed from the low-frequency region of each block. An iterative algorithm is applied to the generated trees until the resulting tree fulfils a requisite criterion. More precisely, the TSVQ tree that matches a particular value of entropy and provides a near-optimal value according to Shannon’s rate-distortion function is selected. The proposed method is shown to be able to preserve the embedded mark under lossy compression (above a given threshold) but, at the same time, it detects possibly forged blocks and their positions in the whole image. Experimental results show how the scheme can be applied to detect forgery attacks, and JPEG2000 compression of the images can be applied without removing the authentication mark. The scheme is also compared to other works in the literature.
A labour of love : 'No schools for medical editors' : correspondence (2013)

The editorial 'No schools for medical editors' struck a personal chord. The lot of the journal editor can indeed be lonely. The challenge of dealing with the manuscripts of colleagues, friends and associates is often fraught with difficulty, especially if one is based at an academic institution where many potential contributors are likely to reside.
Energy and Spectral-Efficient Lens Antenna Subarray Design in MmWave MIMO Systems (2022)

Lens antenna subarray (LAS) is one of the recently introduced technologies for future wireless networks that significantly improves the energy efficiency of multiple-input multiple-output (MIMO) systems while achieving higher spectral efficiency compared to single-lens MIMO systems. However, a control mechanism for the design of LAS-MIMO is considered a challenging task to efficiently manage the network resources and serve multiple users in the system. Therefore, a sub-grouped LAS-MIMO architecture along with a hybrid precoding algorithm are proposed in this paper to reduce the cost and hardware overhead of traditional hybrid MIMO systems. Specifically, the LAS structure is divided into sub-groups to serve multiple users with different requirements, and an optimization problem based on the achievable sum-rate is formulated to maximize the spectral efficiency of the system. By splitting the sum-rate problem into sub-rate optimization problems, we develop a low-complexity hybrid precoding algorithm to effectively control the proposed architecture and maximize the achievable sum-rate of each subgroup. The proposed precoding algorithm selects the beam of each lens from a predefined set within a subgroup that maximizes the subgroup sum-rate, while the phase shifters and digital precoders in each subgroup are computed independently. The link between subgroups is updated based on successive interference cancelation to minimize interference between users of different subgroups. Our analysis and simulation results show that the proposed precoding algorithm of the sub-grouped LAS-MIMO architecture performs almost as well as traditional fully-connected hybrid MIMO systems in terms of spectral efficiency at low and high signal-to-noise ratio (SNR). It also outperforms traditional fully-connected and sub-connected hybrid MIMO systems in terms of energy efficiency, even when a large number of lenses are used.
Defining the Mandate of Tuberculosis Research in a Postgenomic Era (2004)

The identification of &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; by Robert Koch in 1882 as the causative agent of tuberculosis, the release of the drug rifampicin in 1970 and the sequencing of the &lt;i&gt;M. tuberculosis&lt;/i&gt; genome in 1998 are three major events that have revolutionized tuberculosis research. In spite of these breakthroughs, the continued status of tuberculosis as the largest killer amongst infectious diseases is an issue of major concern. Although directly observed short course chemotherapy exists to treat the disease, the emergence of drug-resistant strains has severely threatened the efficacy of the treatment. The recent sequencing of the &lt;i&gt;M. tuberculosis&lt;/i&gt; genome holds promise for the development of new vaccines and the design of new drugs. This is all the more possible when the information from the genome sequence is combined with proteomics and structural and functional genomics. Such an integrated approach has led to the birth of a new field of research christened ‘postgenomics’ that holds substantial promise for the identification of novel drug targets and the potential to aid the development of new chemotherapeutic compounds to treat tuberculosis. The challenge before the scientific community therefore lies in elucidation of the wealth of information provided by the genome sequence and its translation into the design of novel therapies for the disease. All the major developments in the field of tuberculosis research after the sequencing of the &lt;i&gt;M. tuberculosis&lt;/i&gt; genome will be discussed in this review.
Molecular mechanisms of bifunctional vitamin D receptor agonist-histone deacetylase inhibitor hybrid molecules in triple-negative breast cancer (2022)

The active form of vitamin D, 1,25-dihydroxyvitamin D (1,25D), and its analogues signal through the nuclear vitamin D receptor (VDR), a ligand-regulated transcription factor, and have been extensively investigated as anticancer agents. 1,25D and its analogs have potential in combination therapies because they exhibit synergistic activities with other anticancer agents such as histone deacetylase inhibitors (HDACi). We have developed a series of hybrid molecules that combine HDACi within the backbone of a VDR agonist and thus represent fully integrated bifunctional molecules. They exhibit anti-tumor efficacy in reducing tumor growth and metastases in an aggressive model of triple-negative breast cancer. However, their solubility is limited by their hydrophobic diarylpentane cores. Our goals here were two-fold: (1) to improve the solubility of hybrids by introducing nitrogen into diarylpentane cores, and (2) to investigate the molecular mechanisms underlying their anti-tumor efficacy by performing comparative gene expression profiling studies with 1,25D and the potent HDACi suberoylanilide hydroxamic acid (SAHA). We found that substituting aryl with pyrydyl rings did not sacrifice bifunctionality and modestly improved solubility. Notably, one compound, AM-193, displayed enhanced potency as a VDR agonist and in cellular assays of cytotoxicity. RNAseq studies in triple negative breast cancer cells revealed that gene expression profiles of hybrids were very similar to that of 1,25D, as was that observed with 1,25D and SAHA combined. The effects of SAHA alone on gene expression were limited and distinct from those 1,25D or hybrids. The combined results suggest that efficacy of hybrids arises from targeting HDACs that do not have a direct role in gene regulation. Moreover, pathways analysis revealed that hybrids regulate numerous genes controlling immune cell infiltration into tumors and suppress the expression of several secreted molecules that promote breast cancer growth and metastasis.
Clinical relevance of clonal hematopoiesis in persons aged ≥80 years (2021)

Clonal hematopoiesis of indeterminate potential (CHIP) is associated with increased risk of cancers and inflammation-related diseases. This phenomenon becomes common in persons aged ≥80 years, in whom the implications of CHIP are not well defined. We performed a mutational screening in 1794 persons aged ≥80 years and investigated the relationships between CHIP and associated pathologies. Mutations were observed in one-third of persons aged ≥80 years and were associated with reduced survival. Mutations in JAK2 and splicing genes, multiple mutations (DNMT3A, TET2, and ASXL1 with additional genetic lesions), and variant allele frequency ≥0.096 had positive predictive value for myeloid neoplasms. Combining mutation profiles with abnormalities in red blood cell indices improved the ability of myeloid neoplasm prediction. On this basis, we defined a predictive model that identifies 3 risk groups with different probabilities of developing myeloid neoplasms. Mutations in DNMT3A, TET2, ASXL1, or JAK2 were associated with coronary heart disease and rheumatoid arthritis. Cytopenia was common in persons aged ≥80 years, with the underlying cause remaining unexplained in 30% of cases. Among individuals with unexplained cytopenia, the presence of highly specific mutation patterns was associated with myelodysplastic-like phenotype and a probability of survival comparable to that of myeloid neoplasms. Accordingly, 7.5% of subjects aged ≥80 years with cytopenia had presumptive evidence of myeloid neoplasm. In summary, specific mutational patterns define different risk of developing myeloid neoplasms vs inflammatory-associated diseases in persons aged ≥80 years. In individuals with unexplained cytopenia, mutational status may identify those subjects with presumptive evidence of myeloid neoplasms.
Cataract surgical problem: Reply (2002)

Journal of Cataract & Refractive Surgery: October 2002 - Volume 28 - Issue 10 - p 1722-1723 doi: 10.1016/S0886-3350(02)01678-4
Supplementary Figure S4 from EZH2 Inhibition Blocks Multiple Myeloma Cell Growth through Upregulation of Epithelial Tumor Suppressor Genes (2023)

&lt;p&gt;Effects of GSK126 treatment in MOLP-8 cell line&lt;/p&gt;