gebhart/patrepeval huggingface dataset:
Synthesis of Fmoc-Protected Arylphenylalanines (Bip Derivatives) via Nonaqueous Suzuki-Miyaura Cross-Coupling Reactions (2016)

A one-step synthesis of Fmoc-protected aryl/heteroaryl-substituted phenylalanines (Bip derivatives) using the nonaqueous palladium-catalyzed Suzuki-Miyaura cross-coupling (SMC) reaction of Fmoc-protected bromo- or iodophenylalanines is reported. This protocol allows for the direct formation of a variety of unnatural biaryl-containing amino acids in good to excellent yield, which can be readily used in subsequent Fmoc solid-phase peptide synthesis. The synthetic utility of this method is also demonstrated by the SMC reaction of bromophenylalanine-containing tripeptides.
Succinate Dehydrogenase (SDH) D Subunit (SDHD) Inactivation in a Growth-Hormone-Producing Pituitary Tumor: A New Association for SDH? (2011)

We describe the first kindred with a germline SDHD pathogenic mutation, inherited PGL, and acromegaly due to a GH-producing pituitary adenoma. SDHD loss of heterozygosity, down-regulation of protein in the GH-secreting adenoma, and decreased SDH enzymatic activity supports SDHD's involvement in the pituitary tumor formation in this patient. Older cases of multiple PGL and PHEO and pituitary tumors in the literature support a possible association between SDH defects and pituitary tumorigenesis.
Binocular vision and the control of foot placement during walking in natural terrain (2021)

Abstract Coordination between visual and motor processes is critical for the selection of stable footholds when walking in uneven terrains. While recent work (Matthis et al. in Curr Biol 8(28):1224–1233, 2018) demonstrates a tight link between gaze (visual) and gait (motor), it remains unclear which aspects of visual information play a role in this visuomotor control loop, and how the loss of this information affects that relationship. Here we examine the role of binocular information in the visuomotor control of walking over complex terrain. We recorded eye and body movements while normally-sighted participants walked over terrains of varying difficulty, with intact vision or with vision in one eye blurred to disrupt binocular vision. Gaze strategy was highly sensitive to the complexity of the terrain, with more fixations dedicated to foothold selection as the terrain became more difficult. The primary effect of increased sensory uncertainty due to disrupted binocular vision was a small bias in gaze towards closer footholds, indicating greater pressure on the visuomotor control process. Participants with binocular vision losses due to developmental disorders (i.e., amblyopia, strabismus), who have had the opportunity to develop alternative strategies, also biased their gaze towards closer footholds. Across all participants, we observed a relationship between an individual’s typical level of binocular visual function and the degree to which gaze is shifted toward the body. Thus the gaze–gait relationship is sensitive to the level of sensory uncertainty, and deficits in binocular visual function (whether transient or long-standing) have systematic effects on gaze strategy in complex terrains. We conclude that binocular vision provides useful information for locating footholds during locomotion. Furthermore, we have demonstrated that combined eye/body tracking in natural environments can be used to provide a more detailed understanding of the impact of a type of vision loss on the visuomotor control process of walking, a vital everyday task.
Circulating activated innate lymphoid cells and mucosal-associated invariant T cells are associated with airflow limitation in patients with asthma (2016)

For the first time, our data showed that activated NK cells, ILC1s, ILC2s, ILC3s, and MAIT cells were positively correlated with each other and may be associated with airflow limitation in patients with asthma.
Erratum: Neutron Phase Imaging and Tomography [Phys. Rev. Lett.96, 215505 (2006)] (2006)

Received 24 July 2006DOI:https://doi.org/10.1103/PhysRevLett.97.069905©2006 American Physical Society
Photocatalytic properties for different metal-oxide nanomaterials (2019)

We here demonstrate the synthesis of different nanostructures, including nanoparticles, nanorods, core-shell structures, and compound metal oxide nanostructures all synthesized by a low temperature chemical process. We further investigated their photocatalytic properties for degradation of toxic waste and their photochemical efficiency for water splitting. All the photocatalytic properties as well as the photochemical properties were utilized using sun radiation. The results presented indicate huge potential for the investigated processes with positive impact to energy consumption and benefits for the environment.
Fabrication of large-area face-centered-cubic hard-sphere colloidal crystals by shear alignment (2000)

We make hard-sphere colloidal crystals from polymethyl methacrylate spheres suspended in organic solvents at high volume fractions. The samples are crystallized between two glass plates separated by 10-\ensuremath{\mu}m spacer beads. We study the optical scattering from these systems and describe methods for discriminating between the various crystal packings. Crystals formed simply by increasing the volume fraction beyond the liquid-solid phase transition tend to be small and predominantly random close packed. However, we find that by forming these crystals while applying controlled shear to the glass plates, large-area single crystals can be made. These crystals are much more regular and appear to be predominantly twinned face-centred cubic. The creation of single-orientation face-centred cubic crystals appears possible when shear is applied in one direction.
Supplementary Tables from Targeting Bromodomain and Extra-Terminal (BET) Family Proteins in Castration-Resistant Prostate Cancer (CRPC) (2023)

&lt;p&gt;Supplementary Tables 1 to 10 Supplementary Table 1: Cell lines ATCC - american type culture collection, FBS - fetal bovine serum, CSS - charcoal stripped serum, * - LNCaP95 cells were kindly provided by Drs. Alan K Meeker and Jun Luo (Johns Hopkins University, Baltimore, Maryland, USA), NA - non-applicable, ^ - phenol red free, BPE/EGF - bovine pituitary extract and human recombinant epidermal growth factor. Supplementary Table 2: ON-TARGETplus siRNA pools for gene expression knock down Supplementary Table 3: TaqMan probes for qRT-PCR analysis Supplementary Table 4: Primary antibodies for western blot analysis Supplementary Table 5: AR regulated genes included in AR activity score Supplementary Table 6: Patient baseline characteristics at prostate cancer diagnosis N - number, SD - standard deviation, IQR - interquartile range, NR - not recorded, PSA - prostate specific antigen, NA - non-applicable. ^5 patient without PSA values; one value &gt;2000 (analyzed as 2000) *All cases adenocarcinoma 1Student's t-test 2Fisher's Exact Test 3Wilcoxon Rank-Sum Test Supplementary Table 7: Cellular pathways regulated by I-BET151 treatment Cellular pathways annotated by CellMap (C), Reactome (R), KEGG (K), NCI PID (N), Panther (P) and BioCarta (B) with p value &lt;0.005 and false discovery rate (FDR) &lt;0.05 are shown. Supplementary Table 8: Alternative splicing events in response to I-BET151 treatment SE - skipped exons, A5SS - alternative 5â€² splice sites, A3SS - alternative 3â€² splice sites, MXE - mutually exclusive exons, RI - retained introns, FDR - false discovery rate, NRCD - normalized reads count difference. All genes with normalized reads count difference (NRCD) &gt;0.2 and &lt;-0.2, and false discovery rate (FDR) &lt;0.05 highlighted in blue. Supplementary Table 9: Patient derived organoids derived from CRPC biopsies harboring AR aberrations. CRPC - castration resistant prostate cancer, AR - androgen receptor, CN - copy number, AR-V7 androgen receptor variant 7, AR-FL - androgen receptor full length, SPOP - substrate-binding adaptor speckle-type POZ protein, IHC - immunohistochemistry H-score. *Mutational, CN analysis or IHC performed on same patient but alternative metastatic biopsy Supplementary Table 10: Patient baseline characteristics at prostate cancer diagnosis. N - number, SE - standard error, NR - not recorded, PSA - prostate specific antigen. *one patient received curative therapy (with oligo-metastatic disease) ^one patient received docetaxel in hormone sensitive setting 1Fisher's Exact Test 2Wilcoxon Rank-Sum Test&lt;/p&gt;
ChemInform Abstract: Defect Chemistry in Ferroelectric Perovskites: Long Standing Issues and Recent Advances (2015)

Abstract Review: 42 refs.
Vertex Feature Encoding and Hierarchical Temporal Modeling in a Spatio-Temporal Graph Convolutional Network for Action Recognition (2021)

Spatio-temporal Graph Convolutional Networks (ST-GCNs) have shown great performance in the context of skeleton-based action recognition. Nevertheless, ST-GCNs use raw skeleton data as vertex features. Such features have low dimensionality and might not be optimal for action discrimination. Moreover, a single layer of temporal convolution is used to model short-term temporal dependencies but can be insufficient for capturing both long-term. In this paper, we extend the Spatio-Temporal Graph Convolutional Network for skeleton-based action recognition by introducing two novel modules, namely, the Graph Vertex Feature Encoder (GVFE) and the Dilated Hierarchical Temporal Convolutional Network (DH-TCN). On the one hand, the GVFE module learns appropriate vertex features for action recognition by encoding raw skeleton data into a new feature space. On the other hand, the DH-TCN module is capable of capturing both short-term and long-term temporal dependencies using a hierarchical dilated convolutional network. Experiments have been conducted on the challenging NTU RGB-D 60, NTU RGB-D 120 and Kinetics datasets. The obtained results show that our method competes with state-of-the-art approaches while using a smaller number of layers and parameters; thus reducing the required training time and memory.
Antennas on Silicon: Hybrid integration versus SoC solutions? (2012)

Silicon technologies are now competitive with III-V components for applications in the millimeter wave frequencies range, as already demonstrated through fully integrated on-chip systems [1]-[6]. We discuss in this paper of the different thinkable alternative solutions to fully implement efficient antennas within Silicon environment, exploiting either SoC (System on Chip) or SiP (System in Package) approaches depending on the expected performances.
ard-1: a human gene that reverses the effects of temperature-sensitive and deletion mutations in the Escherichia coli rne gene and encodes an activity producing RNase E-like cleavages. (1994)

The Escherichia coli rne gene affects a variety of bacterial functions, including the activity of RNase E. We report the existence of a human gene (ard-1, for activator of RNA decay) that complements temperature-sensitive and deletion mutations of rne in E. coli, allowing growth of rne-defective cells, correcting abnormal cell shape, activating chemical decay of bulk mRNA, and producing site-specific cleavages characteristic of RNase E in vivo and in vitro. ard-1 encodes a highly basic 13.3-kDa proline-rich peptide that has features in common with Rne and also with eukaryotic proteins implicated in RNA binding and macromolecular transport.
Potential Therapeutic Advantages of Doxorubicin when Activated by Formaldehyde to Function as a DNA Adduct-Forming Agent (2015)

Doxorubicin has been in use as a key anticancer drug for forty years, either as a single agent or in combination chemotherapy. It functions primarily by interfering with topoisomerase II activity but in the presence of formaldehyde, it forms adducts with DNA, mainly with the exocyclic amine of guanine at GpC sites and these adducts are more cytotoxic than topoisomerase II induced damage. High levels of adducts form spontaneously from the endogenous level of formaldehyde in tumour cells (1,300 adducts per cell after a 4 hr treatment with doxorubicin), but substantially higher levels form with the addition of exogenous sources of formaldehyde, such as formaldehyde releasing prodrugs. The enhanced cytotoxicity of adducts has been confirmed in mouse models, with adduct-forming conditions resulting in much improved inhibition of tumour growth, as well as cardioprotection. Doxorubicin cardiotoxicity has been attributed to topoisomerase II poisoning, and the cardioprotection is consistent with a mechanism switch from topoisomerase II poisoning to covalent adduct formation. Although the adducts have a half-life of less than one day, a population remains as essentially permanent lesions. The capacity of doxorubicin to form adducts offers a range of potential advantages over the conventional use of doxorubicin (as a topoisomerase II poison), including: enhanced cell kill; tumour-selective activation, hence tumour-selective cell kill; decreased cardiotoxicity; decreased resistance to prolonged doxorubicin treatment. There is therefore enormous potential to improve clinical responses to doxorubicin by using conditions which favour the formation of doxorubicin-DNA adducts.
Atopic Dermatitis-Like Non-Erythrodermic Leukemic Variant of CD3−/+dimCD4+Cutaneous T-Cell Lymphoma Preceded by Cutaneous Papular Xanthomatosis (2003)

We report a patient with cutaneous papular xanthomatosis who 4 years later developed a CD3(-/+dim)/CD4(+) T-cell lymphoma. Pruritic xerotic non-erythrodermic skin, eosinophilia and hyper-IgE were present and erroneously classified as atopic dermatitis. Flow cytometry and DNA ploidy analysis of both blood and skin lymphocytes, skin histology and blood T-cell receptor gene rearrangement studies confirmed diagnosis of T-cell lymphoma. Monoclonal CD3(-/+dim)/CD4(+) T-cells were especially prone to the synthesis of IL-13, a cytokine that is involved in IgE-secretion, and comprised both a medium (diploid) and large (hyperploid) sized T-cell populations with a similar immunophenotype. The majority of the normal residual T-cells were large granular lymphocytes, expressed activation-related and natural-killer-associated markers and secreted high levels of interferon gamma, suggesting that they might correspond to active cytotoxic cells directed against the neoplastic T-lymphocytes.
Visualization of directed associations in e-commerce transaction data (2001)

Many real-world e-commerce applications require the mining of large volumes of transaction data to extract marketing and sales information. This paper describes the Directed Association Visualization (DAV) system that visually associates product affinities and relationships for large volumes of e-commerce transaction data. DAV maps transaction data items and their relationships to vertices, edges, and positions on a visual spherical surface. DAV encompasses several innovative techniques (1) items are positioned according to their associations to show the strength of their relationships; (2) edges with arrows are used to represent the implication directions; (3) a mass-spring engine is integrated into a visual data mining platform to provide a self-organized graph. We have applied this system successfully to market basket analysis and e-customer profiling Internet applications.
Novel subspace methods for blind estimation of multiple CFOs in MIMO-OFDM systems (2010)

The problem of estimating multiple Carrier Frequency Offsets (CFOs) in the uplink of MIMO-OFDM systems with Co-Channel (CC) and OFDMA based carrier allocation is considered. The tri-linear data model for generalized, multiuser OFDM system is formulated. Novel blind subspace based estimation of multiple CFOs in the case of arbitrary carrier allocation scheme in OFDMA systems and CC users in OFDM systems based on the Khatri-Rao product is proposed. The method works where the conventional subspace method fails. The performance of the proposed methods is compared with pilot based Least-Squares method.
Neuroprotective Effect of a New Synthetic Aspirin-decursinol Adduct in Experimental Animal Models of Ischemic Stroke (2013)

Stroke is the second leading cause of death. Experimental animal models of cerebral ischemia are widely used for researching mechanisms of ischemic damage and developing new drugs for the prevention and treatment of stroke. The present study aimed to comparatively investigate neuroprotective effects of aspirin (ASA), decursinol (DA) and new synthetic aspirin-decursinol adduct (ASA-DA) against transient focal and global cerebral ischemic damage. We found that treatment with 20 mg/kg, not 10 mg/kg, ASA-DA protected against ischemia-induced neuronal death after transient focal and global ischemic damage, and its neuroprotective effect was much better than that of ASA or DA alone. In addition, 20 mg/kg ASA-DA treatment reduced the ischemia-induced gliosis and maintained antioxidants levels in the corresponding injury regions. In brief, ASA-DA, a new synthetic drug, dramatically protected neurons from ischemic damage, and neuroprotective effects of ASA-DA may be closely related to the attenuation of ischemia-induced gliosis and maintenance of antioxidants.
Abstract MP166: PRKAR1A Deficiency Abrogates Cardiac Hypertrophy Through Inhibition of Mitochondrial Fission (2020)

Protein kinase A (PKA) is pivotal for cardiac function of human heart, and its dysregulation is involved with various cardiac pathologies. PKA regulatory subunit 1α (R1α, encoded by PRKAR1A gene) controls PKA kinase activity by sequestering the PKA catalytic subunits. Patients with PRKAR1A mutations are often diagnosed with Carney complex (CNC) and may die prematurely from cardiac complications such as heart failure. However, it remains unknown whether PRKAR1A deficiency interferes with normal heart growth during postnatal development. Here, we show that left ventricular mass is reduced in young CNC patients with PRKAR1A mutations or deletions. To investigate the impact of PRKAR1A deficiency on heart growth, we generated cardiac-specific PRKAR1A heterozygous knockout mice. Ablation of the PRKAR1A gene in mice increased cardiac PKA activity, reduced heart weight to body weight ratio and cardiomyocyte size without altering contractile function. Cardiomyocyte hypertrophy in response to activation of the α1-adrenergic receptor, was completely abolished by silencing of PRKAR1A . Mechanistically, depletion of PRKAR1A provoked PKA-dependent phosphorylation of the mitochondrial fission protein Drp1 at S637, resulting in impaired mitochondrial fission and diminished cardiomyocyte hypertrophy. In conclusion, PRKAR1A deficiency abrogates cardiac hypertrophy during postnatal development, likely through inhibiting Drp1-mediated mitochondrial fission. Our study provides novel mechanistic insights regarding the cardiac mortality associated with CNC.
Aromatase and testosterone fatty acid esters: the search for a cryptic biosynthetic pathway to estradiol esters (1992)

The estradiol fatty acid esters (lipoidal derivatives, LE2) are extremely potent estrogens that accumulate in fat, including fat of menopausal women. These steroidal esters are protected from metabolism and are converted to the free, biologically active steroid through the action of esterases. Previous studies have shown that biosynthetic pathways in the adrenal gland exist in which steroid fatty acid esters are substrates. This led us to determine whether a cryptic aromatase pathway exists in which testosterone esters could be converted directly into LE2. We tested a representative fatty acid ester, testosterone stearate, both as an inhibitor and as a substrate for the aromatase enzyme from human placental microsomes. This ester had neither activity. In addition, we tested [1 beta-3H]testosterone acetate as a substrate for this enzyme complex, measuring the production of 3H2O as evidence of aromatization. Although the rate of reaction was considerably slower than that of testosterone, 3H2O was produced. However, when [2, 4, 6, 7-3H]testosterone acetate was incubated and the steroidal products isolated, we found that hydrolysis of the substrate had occurred. Both [3H]-labeled testosterone and estradiol were found, and very little if any [3H]estradiol acetate was formed. Thus, we conclude that an aromatase pathway involving testosterone esters does not exist and that the sole source of LE2 is through direct esterification of estradiol.
Randomization techniques for assessing the significance of gene periodicity results (2011)

Existing methods for testing significance of periodic gene expression patterns are simplistic and optimistic. Our testing framework allows strict levels of statistical significance with more realistic underlying assumptions, without losing predictive power. As DNA microarrays have now become mainstream and new high-throughput methods are rapidly being adopted, we argue that not only there will be need for data mining methods capable of coping with immense datasets, but there will also be need for solid methods for significance testing.
Asian consensus on the relationship between obesity and gastrointestinal and liver diseases (2016)

The incidence of obesity is increasing in Asia, with implications on gastrointestinal (GI) and liver diseases. The Gut and Obesity in Asia Workgroup comprises regional experts with the aim of studying relationship between obesity and the GI and liver diseases in Asia. Through literature review and the modified Delphi process, consensus statements examining the impact of obesity on esophageal, gastric, pancreatic, colorectal, and liver diseases, exploring relationship between gut microbiome and obesity, and assessing obesity therapies have been produced by the Gut and Obesity in Asia Workgroup. Sixteen experts participated with 9/15 statements having strong consensus (>80% agreement). The prevalence of obesity in Asia is increasing (100% percentage agreement in brackets), and this increased prevalence of obesity will result in a greater burden of obesity-related GI and liver diseases (93.8%). There was consensus that obesity increases the risk of gastric cancer (75%) and colorectal neoplasia (87.5%). Obesity was also associated with Barrett's esophagus and esophageal adenocarcinoma (66.7%) and pancreatic cancer (66.7%) in Asia. The prevalence of non-alcoholic fatty liver disease (NAFLD) in Asia is on the rise (100%), and the risk of NAFLD in Asia (100%) is increased by obesity. Obesity is a risk factor for the development of hepatocellular carcinoma (93.8%). Regarding therapy, it was agreed that bariatric surgery was an effective treatment modality for obesity (93.8%) but there was less agreement on its benefit for NAFLD (62.5%). These experts' consensus on obesity and GI diseases in Asia forms the basis for further research, and its translation into addressing this emerging issue.