gebhart/patrepeval huggingface dataset:
Improving Knowledge Distillation of CTC-Trained Acoustic Models With Alignment-Consistent Ensemble and Target Delay (2020)

Knowledge distillation (KD) has been widely used to improve the performance of a simpler student model by imitating the outputs or intermediate representations of a more complex teacher model. The most commonly used KD technique is to minimize a Kullback-Leibler divergence between the output distributions of the teacher and student models. When it is applied to compressing acoustic models trained with a connectionist temporal classification (CTC) criterion, an assumption is made that the teacher and student share the same frame-level feature-transcription alignment. However, frame-level alignments learned by teachers can be inaccurate and unstable due to the lack of fine-grained frame-level guidance during CTC training. Forcing student to learn inaccurate alignments will lead to limited performance improvements. In this article, we investigate building powerful teacher models with more accurate and stable feature-transcription alignments. We achieve this goal by using a novel alignment-consistent ensemble (ACE) technique, where all models within an ensemble are jointly trained along with a regularization term to encourage consistent and stable alignments. With well-trained deep bidirectional LSTM (DBLSTM) ACE as a teacher, we can directly use the traditional frame-wise KD method to train DBLSTM students. When applying KD to transfer knowledge from a DBLSTM ACE to a deep unidirectional LSTM (DLSTM) student, a simple yet effective target delay technique is proposed to handle the alignment difference between bidirectional and unidirectional models. Experimental results on Switchboard-I speech recognition task show that, with DBLSTM ACE as a teacher, the simple frame-wise KD method can achieve competitive or better performance than other complex KD methods on DBLSTM students. When applying KD to build DLSTM students from DBLSTM teachers, our proposed target delay technique can achieve relative word error rate reductions of 14.2%$\sim$14.8% compared with the models trained from scratch, which outperforms other carefully-designed KD methods.
Type IV collagenase activity of a primary HSV-2-induced hamster fibrosarcoma and itsin vivo metastases andin vitro clones (1987)

The expression of a basement membrane (BM) collagen-degrading metalloprotease (Type IV collagenase) was studied in a herpes simplex virus (HSV)-2 transformed hamster fibrosarcoma and its in vivo derived sublines and in vitro derived clones of varying metastatic potential. The primary parent tumor was shown to release more or less Type IV collagenolytic activity compared with its sublines (derived from lung nodules that developed after resection of the primary tumor). Normal baby hamster kidney and hamster embryo fibroblasts did not secrete detectable amounts of BM collagenase, whereas normal hamster lung fibroblast secreted intermediate levels of Type IV collagenase activity. The collagenase IV activity of the parent tumor and its in vivo and in vitro derived sublines was assayed in vitro and compared with the ability of the cells lines to spontaneously metastasize in vivo. No correlation between the ability to secrete type IV collagenase and metastatic propensity was detected. Although all cell lines secreted type IV collagenase, the highest activity was recorded for a nonmetastatic variant.
Wideband circular polarized Fabry-Perot cavity antennas for V-band indoor point-to-point communications (2018)

In this paper, a 60 GHz planar Fabry-Perot cavity (FPC) antenna with a circularly polarized (CP) radiation characteristic is proposed as a good candidate for millimeter-wave wireless systems. A sparse array design is employed to enhance the gain bandwidth (GBW) product of the antenna. Complete formulations for circular polarized radiation are developed to serve as a general guideline scalable to any frequencies. The theoretical results using ideal point sources are validated by numerical analysis using the finite elements method (FEM). In the full-wave simulations, the ideal sources are replaced by four annular-ring slot antennas to excite the FPC.
Immobilized phenylalanine hydroxylase through the SH groups (1986)

Purified rat liver phenylalanine hydroxylase [L-phenylalanine:tetrahydropteridine:oxygen oxidoreductase (4-hydroxylating), EC 1.14.16.1] was immobilized with activated thiol-Sepharose 4B via disulfide bond formation, which is expected to immobilize the enzyme in its activated form through the SH modification. This immobilized enzyme was more stable against thermal denaturation than the free enzyme. When tetrahydrobiopterin was used as the natural cofactor, the K(m) value for phenylalanine was decreased and that for the cofactor was increased. Constant conversion from phenylalanine to tyrosine was demonstrated continuously for over 8 h at 25 degrees C.
Treatment of Macular Edema following Branch Retinal Vein Occlusion (2013)

Branch retinal vein occlusion (BRVO) is a relatively prevalent cause of reduced vision primarily due to macular edema. Vascular endothelial growth factor (VEGF) is the major stimulator of excessive vascular leakage and also contributes to retinal hemorrhages and progressive retinal nonperfusion (RNP). Progressive RNP results in worsening of retinal ischemia further increasing levels of VEGF, resulting in a positive feedback loop for disease worsening over time. Aggressive early treatment with a specific antagonist of VEGF causes rapid improvement in edema and visual acuity, speeds resolution of hemorrhages, and stabilizes or improves RNP. Therefore, first-line treatment of acute BRVOs is monthly injections of an anti-VEGF agent for at least 6 months. After that, a period of monthly follow up with anti-VEGF treatment, only if there is recurrent edema, can be used to gauge persistent disease activity and the need for grid laser photocoagulation to diffuse leakage in the macula outside the foveal avascular zone. Following grid laser, another period of monthly follow up with anti-VEGF treatment only if there is recurrent edema provides a measure of persistent disease activity, and if frequent injections are still needed to control edema, the benefits and risks for switching to dexamethasone implants should be discussed with the patient.
Length rather than a specific allele of dinucleotide repeat in the 5′ upstream region of the aldose reductase gene is associated with diabetic retinopathy (1999)

(CA)n repeat length, rather than a specific allele, in the 5' upstream region of the AR gene is associated with diabetic retinopathy. These data suggest that the AR locus plays a role in genetic susceptibility to diabetic retinopathy and that dinucleotide repeats in genomic DNA may be related to disease predisposition.
High serum interleukin‐6 level predicts future hepatocellular carcinoma development in patients with chronic hepatitis B (2009)

Increased interleukin-6 (IL-6) production is implicated in the pathogenesis of hepatocellular carcinoma (HCC) in animal models. Although previous studies showed that HCC patients had higher serum IL-6 level at the time of diagnosis, it is unclear if the cytokine contributes to the development of HCC or is just a reaction to cancer. To address this question, we performed a nested case-control study. Consecutive chronic hepatitis B patients were recruited from 1997 to 2000 and followed till 2008. Profiling of 27 cytokines, chemokines and growth factors was performed at baseline, date of peak alanine aminotransferase (ALT) level and the last visit. Thirty-seven patients developed HCC at a median follow-up of 62 months (interquartile range: 41-110). Serum IL-6 was higher in patients with HCC than controls both during peak ALT and at the last visit (both p = 0.02). Patients with IL-6 above 7 pg/ml during peak ALT had increased risk of HCC or death (adjusted hazard ratio 3.0; 95% confidence interval 1.2, 7.8; p = 0.02). The sensitivity, specificity, positive and negative predictive values of this cutoff to predict future HCC development were 70%, 73%, 72% and 71%, respectively. Combination of IL-6 and AFP improved the sensitivity in diagnosing HCC or predicting future HCC development. In conclusion, high serum IL-6 level predates the development of HCC in chronic hepatitis B patients, and has moderate accuracy in predicting future cancer. This may assist clinicians in selecting high-risk patients for HCC surveillance program.
Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer (2017)

Prostate cancer is the second leading cause of male cancer deaths due to disease progression to castration-resistant prostate cancer (CRPC). Androgen receptor (AR) splice variants including AR-V7 function as constitutively active transcription factors in CRPC cells, thereby promoting resistance to AR-targeted therapies. To date, there are no AR variant-specific treatments for CRPC. Here we report that the splicing of AR variants AR-V7 as well as AR-V1 and AR-V9 is regulated coordinately by a single polyadenylation signal in AR intron 3. Blocking this signal with morpholino technology or silencing of the polyadenylation factor CPSF1 caused a splice switch that inhibited expression of AR variants and blocked androgen-independent growth of CRPC cells. Our findings support the development of new therapies targeting the polyadenylation signal in AR intron 3 as a strategy to prevent expression of a broad array of AR variants in CRPC. <i>Cancer Res; 77(19); 5228-35. ©2017 AACR</i>.
Contribution of immunoglobulin lambda light chain gene rearrangement analysis in the diagnosis of B‐cell neoplasms (2019)

Identification of clonal IGH, IGK and IGL gene rearrangements offers diagnostic adjunct in suspected B-cell neoplasms. However, many centres omit IGL analysis as its value is uncertain. A review of 567 cases with IGH, IGK and IGL rearrangement assessed using BIOMED-2 assays showed clonal immunoglobulin gene rearrangement in 54% of cases, of which 24% had a clonal IGL rearrangement. In two cases, the clonal rearrangement was detected exclusively by IGL analysis. This finding demonstrates the added value of IGL analysis for clonality assessment, especially in suspected B-cell neoplasms in which a clonal IGH and/or IGK rearrangement is not detected or is equivocal.
Single-cell expression profiling of human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence (2006)

Considerable progress has been made in characterizing epidermal stem cells by microarray analysis of FACS-selected populations. One limitation of this approach is that the gene expression profiles represent the average of the cell population, potentially masking cellular heterogeneity of functional significance. To overcome this problem, we have performed single-cell expression profiling. We have generated cDNA libraries from single human epidermal cells, designated as stem or transit-amplifying cells on the basis of Delta1 and melanoma-associated chondroitin sulfate proteoglycan expression. Of the 14 putative stem cell markers identified, we selected one, the EGF receptor antagonist leucine-rich repeats and immunoglobulin-like domains 1 (Lrig1), for further study. Lrig1 was expressed in groups of basal cells in human interfollicular epidermis previously identified as enriched for stem cells. Overexpression of Lrig1 decreased keratinocyte proliferation but did not affect the proportion of stem and transit-amplifying cells, as judged by clonal growth characteristics. Down-regulation of Lrig1 using siRNA increased cell-surface EGF receptor levels, enhanced activation of downstream pathways, and stimulated proliferation. Lrig1 acted in part by negatively regulating the Myc promoter. We propose that Lrig1 maintains epidermal stem cells in a quiescent nondividing state, and that Lrig1 down-regulation triggers proliferation.
Polar effects in free-radical reactions. Carbamoylation and .alpha.-N-amidoalkylation of heteroaromatic bases by amides and hydroxylamine-O-sulfonic acid (1984)

NH3+·, formed in the decompn. of H3N+OSO3- by Fe2+, generates carbamoyl and α-N-amidoalkyl radicals by H abstraction from formamide, alkylformamides, and N-alkylacetamides. Both carbamoyl and α-N-amidoalkyl radicals have a clear-cut nucleophilic character and selectively attack protonated heteroarom. bases, e.g., 4-methylquinoline or quinoxaline, in the α-position or are oxidized by Fe(III) salts. Redox chain mechanisms are involved. The importance of the polar effects in the H abstraction, arom. substitution, and oxidn. by Fe(III) salt is discussed
Tribochemistry and material transfer for the ultrananocrystalline diamond-silicon nitride interface revealed by x-ray photoelectron emission spectromicroscopy (2007)

The authors report tribochemical changes due to sliding of a silicon nitride (Si3N4) ball against an ultrananocrystalline diamond (UNCD) thin film. Unidirectional sliding wear measurements were conducted for 2000cycles using a ball-on-disk apparatus with a 3∕16in. diameter Si3N4 ball at a sliding speed of 3.3mm∕s and a normal load of 98.0mN (nominal Hertzian stress of 0.6GPa) in a nitrogen environment at 50% relative humidity at room temperature. The wear track produced on the UNCD film was analyzed by X-ray photoelectron emission spectromicroscopy (X-PEEM) combined with X-ray absorption near-edge structure (XANES) spectroscopy to identify and spatially resolve chemical changes inside the wear track, particularly rehybridization of carbon. XANES spectra show that SiOx complexes are deposited within the wear track. Very little rehybridization of the UNCD from its primarily sp3 bonding configuration to sp2 bonding is observed, and there is no observable oxidation of the UNCD, pointing to the impressive stability of the film under significant tribological loading conditions. Raman spectroscopy of the worn portion of the Si3N4 ball shows that disordered carbon is found on the worn surface. The authors attribute the formation of SiOx complexes within the wear track to wear of the ball and subsequent deposition into the track. The authors attribute the disordered carbon on the Si3N4 ball to removal of sp2-bonded carbon from the UNCD surface and subsequent accumulation onto the ball’s surface. This work demonstrates the potential of X-PEEM for the study of tribochemical modifications of carbon-based thin film surfaces.
Domain Cross-talk during Effector Binding to the Multidrug Binding TTGR Regulator (2010)

A major mechanism of antibiotic resistance in bacteria is the active extrusion of toxic compounds through membrane-bound efflux pumps. The TtgR protein represses transcription of ttgABC, a key efflux pump in Pseudomonas putida DOT-T1E capable of extruding antibiotics, solvents, and flavonoids. TtgR contains two distinct and overlapping ligand binding sites, one is broad and contains mainly hydrophobic residues, whereas the second is deep and contains polar residues. Mutants in the ligand binding pockets were generated and characterized using electrophoretic mobility shift assays, isothermal titration calorimetry, and promoter expression. Several mutants were affected in their response to effectors in vitro: mutants H70A, H72A, and R75A did not dissociate from promoter DNA in the presence of chloramphenicol. Other mutants exhibited altered binding to the operator: L66A and L66AV96A mutants bound 3- and 15-fold better than the native protein, whereas the H67A mutant bound with 3-fold lower affinity. In vivo expression assays using a fusion of the promoter of ttgA to lacZ and antibiotic tolerance correlated with the in vitro observations, namely that mutant H67A leads to increased basal expression levels and enhances antibiotic tolerance, whereas mutants L66A and L66AV96A exhibit lower basal expression levels and decreased resistance to antibiotics. The crystal structure of TtgR H67A was resolved. The data provide evidence for the inter-domain communication that is predicted to be required for the transmission of the effector binding signal to the DNA binding domain and provide important information to understand TtgR/DNA/effector interactions.
Tumor Control Index: a novel tool to assess and compare tumor growth in experimental animals (2017)

Abstract Measurement of tumor diameters, tumor volumes, or area under the curve has been traditionally used to quantitate the effects of experimental manipulations in immune competent as well as immune-compromised mice and rats. However, using these parameters to measure the kinetics of tumor growth fail to reveal several complexities of growing tumors. Here, by means of tumor growth data from a large number of mice challenged with live tumor cells, we describe the use of a new composite parameter, Tumor Control Index (TCI) as an alternative method to do the same. This index, comprised of three distinct values, the Tumor Progression Score, Tumor Rejection Score, and Tumor Stability Score, provides a complete picture of nearly every aspect of tumor growth in large numbers of animals, can be deduced automatically from tumor diameter or volume data, and can be used to compare several groups of animals in different experiments. This automatically derivable index also corresponds neatly to the use of complete and partial responses and tumor stability data generated in human tumors, and can be used to assess the efficacy of interventions to be used in clinical studies.
Applied optimal control for dynamically stable legged locomotion (2004)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.
CATHI - TRAINING ON VIRTUAL PATIENTS FOR CATHETER INTERVENTIONS (2002)

In this paper we present a trainings system for catheter interventions, especially PCTAs also called ballon dilatation. Despite the large number of such interventions the education of the cardiologist is still based on learning on the patient. This means risk to the patient and additional cost. To overcome these problems we developed the CathI system (Catheter Instruction System), a realistic computerbased training system. It provides the physician with the same equipment found in a catheter laboratory, e.g. original control instruments for the flouroscopy system, syringes, catheters, and guide wires. CathI only replaces patient and C-arm by a virtual patient and a virtual x-ray system.
Equivalent internal noise for contour integration (2017)

Oriented wavelets give the percept of a contour if each wavelet has the appropriate position and orientation to belong to that contour. The rules governing this have been tested using a contour integration task: observers detect a contour of aligned wavelets buried in a background noise of randomly-oriented wavelets. Here we present a new threshold contour task that does not rely on a background noise field to limit performance. Observers discriminate which of four contours (at an eccentricity of 2.8 degrees in four quadrants) contains the appropriate conjunction of (6 c/deg log-Gabor) wavelet positions and orientations to feature "good continuation". The other three contours have orientations appropriate to the opposite direction of curvature. Thresholds are measured as a function of curvature (straighter contours are more difficult). By corrupting the orientation and position of the individual wavelets with external noise we measured noise masking functions. Both orientation and position noise elevated thresholds. Equivalent internal noise values were compared to those from tasks where observers made judgements about single elements. We found that in a contour the orientation noise was elevated (260%) but the position noise was reduced (40%). This suggests that contour processing privileges the refinement of position information at the expense of orientation. The sensitivity loss between 4 and 8 degrees of eccentricity was modest (10% threshold increase), and was abolished when the scale of the contours was doubled in the periphery. In another experiment, we introduced a "baseline" curvature to the stimuli to investigate discrimination of curvier contours. Thresholds were elevated relative to discrimination of straighter contours (190%). Contrary to results from the previous contour task, we found observers could integrate curvy contours in the periphery. The measurements from this novel paradigm could be used to investigate mid-level visual impairments, and to constrain models of the traditional contour task. Meeting abstract presented at VSS 2017
On the MAC Layer Performance of Time-Hopped UWB Ad Hoc Networks (2006)

Ultra Wide Band (UWB) is a promising technology for short-range wireless networks. In this paper we present our efforts on investigating the impact of the multipath delay spread on the MAC layer performance of time-hopped impulse-based UWB ad hoc networks. We discuss a simplified channel model for the multipath delay spread and we simulate a single-band MAC protocol which employs binary pulse position modulation. Our simulation results demonstrate that the performance is determined by the properties of the time hopping sequences of the nodes. We observe that the right parameter values depend on the number of nodes deployed, and the delay spread experienced. If the topology changes dynamically, adaptive strategies for varying system parameters are required for achieving the best performance.
The Role of BRCA1/BARD1 Heterodimers in the Mitosis-Interphase Transition (2007)

Abstract : The study was aimed at exploiting the advantages of the Xenopus egg extract as a biochemically tractable in vitro cell cycle model system in order to elucidate the molecular function of the breast and ovarian tumor suppressor BRCA1 and its hetorodimerizing partner, BARD1. Experiments using both egg extracts and cultured mammalian cells revealed a previously unknown role of BRCA1/BARD1 in the mitotic spindle assembly. This BRCA1/BARD1 function is centrosome-independent, operates downstream of Ran GTPase, and depends upon the E3 ubiquitin ligase activity of the heterodimer. BRCA1/BARD1 ensures proper spindle pole formation by down-modulating the function of a recently discovered TPX2 partner, XRHAMM, thereby facilitating the accumulation of TPX2, the major spindle assembly factor and Ran target, on spindle poles. Our study implicated BRCA1/BARD1 in the regulation of three SAFs (RHAMM, TPX2, and Aurora A), which are overexpressed or amplified in certain cancers, thus pointing to the existence of a tumor suppressoroncoprotein network that controls mitotic spindle assembly.
Synthesis of Simple Multivalent β-D-GalNAc-(1→4)-β-D-Gal Oligomers as Probes for Investigating the Interactions ofP. AeruginosaPili with Multivalent Receptors (1999)

ABSTRACT Five multivalent β-D-GalNAc-(1→4)-β-D-Gal oligomers were selected and synthesized as probes for investigating the adhesin-receptor interactions of P. aeruginosa pili with multivalent receptors. They were synthesized by the amide coupling reactions of 8-(N-2-aminoethyl)carboxamidooctyl 4-O-(2-acetamido-2-deoxy-β-D-galactopyranosyl)-β-D-galactopyranoside (7) with EDTA dianhydride, EDTA, Kemp's triacid and adipic acid with EDC, DIC and DCC combined with HOBt as coupling reagents and by the reaction of per-O-acetylated 7 with 1,3,5-benzenetricarbonyl trichloride followed by de-O-acetylation. These resulting multivalent compounds contain flexible C9 spacer arms as linkers attached to either flexible hydrophilic moieties or rigid hydrophobic cores.