gebhart/patrepeval huggingface dataset:
Automated Analysis of Low-Field Brain MRI in Cerebral Malaria (2022)

A central challenge of medical imaging studies is to extract biomarkers that characterize disease pathology or outcomes. Modern automated approaches have found tremendous success in high-resolution, high-quality magnetic resonance images. These methods, however, may not translate to low-resolution images acquired on magnetic resonance imaging (MRI) scanners with lower magnetic field strength. In low-resource settings where low-field scanners are more common and there is a shortage of radiologists to manually interpret MRI scans, it is critical to develop automated methods that can augment or replace manual interpretation, while accommodating reduced image quality. We present a fully automated framework for translating radiological diagnostic criteria into image-based biomarkers, inspired by a project in which children with cerebral malaria (CM) were imaged using low-field 0.35 Tesla MRI. We integrate multiatlas label fusion, which leverages high-resolution images from another sample as prior spatial information, with parametric Gaussian hidden Markov models based on image intensities, to create a robust method for determining ventricular cerebrospinal fluid volume. We also propose normalized image intensity and texture measurements to determine the loss of gray-to-white matter tissue differentiation and sulcal effacement. These integrated biomarkers have excellent classification performance for determining severe brain swelling due to CM.
A flexible top metal structure to improve ultra low-k reliability (2015)

High stresses generated from chip-package interactions (CPI), especially when large die is flip mounted on organic substrate using Pb-free C4 bumps, can easily cause low-k delamination. A novel scheme by applying an elastic material can effectively reduce the transmitted stresses and, thus, resolve the interfacial delamination issue. Along with an optimized chip-package integration solution, a reliable interconnect structure with good electrical performance, has been successfully demonstrated.
X chromosome-specific cDNA arrays: identification of genes that escape from X-inactivation and other applications (2001)

Mutant alleles are frequently characterized by low expression levels. Therefore, cDNA array-based gene expression profiling may be a promising strategy for identifying gene defects underlying monogenic disorders. To study the potential of this approach, we have generated an X chromosome-specific microarray carrying 2423 cloned cDNA fragments, which represent up to 1317 different X-chromosomal genes. As a prelude to testing cell lines from patients with X-linked disorders, this array was used as a hybridization probe to compare gene expression profiles in lymphoblastoid cell lines from normal males, females and individuals with supernumerary X chromosomes. Measurable hybridization signals were obtained for more than half of the genes represented on the chip. A total of 53 genes showed elevated expression levels in cells with multiple X chromosomes and many of these were found to escape X-inactivation. Moreover, the detection of a male-viable deletion encompassing three genes illustrates the utility of this array for the identification of small unbalanced chromosome rearrangements.
High-Isolation SAW Duplexer With On-Chip SAW Compensation Circuit Optimized for Isolated Multiple Frequency Bands (2019)

This article describes the simulation analysis and experimental verification of a new type of high-isolation surface-acoustic wave (SAW) duplexer by using an SAW on-chip compensation circuit designed to cancel the leakage signal of the main SAW duplexer at multiple frequency bands. First, an analysis of amplitude and phase change of the SAW duplexer consists of a ladder-type transmitter (Tx) filter, and the double-mode SAW (DMS) receiver (Rx) filter is applied to clarify the cancellation conditions. Then, the feasibility of the SAW compensation circuit using a three-interdigital transducer (IDT) DMS resonator specially designed to satisfy the cancellation conditions is studied in circuit simulation based on the coupling-of-mode (COM) theory. Finally, we analyzed this concept in detail for a long-term-evolution (LTE) Band-I SAW duplexer for Tx and Rx band isolation in both a circuit simulation and experiment. Results showed that around 10-dB improvement of isolation in both the Tx and Rx bands was obtained without sacrificing other properties (e.g., insertion loss and attenuation) and that it agrees well with the result obtained by simulation analysis. These results are expected to be useful for now, considering that future mobile systems demand higher Rx sensitivity in multiple frequency bands.
DeepDraper: Fast and Accurate 3D Garment Draping over a 3D Human Body (2021)

Draping a 3D human mesh has garnered broad interest due to its wide applicability in virtual try-on, animations, etc. The 3D garment deformations produced by the existing methods are often inconsistent with the body shape, pose, and measurements. This paper proposes a single unified learning-based framework (DeepDraper) to predict garment deformation as a function of body shape, pose, measurements, and garment styles. We train the DeepDraper with coupled geometric and multi-view perceptual losses. Unlike existing methods, we additionally model garment deformations as a function of standard body measurements, which generally a buyer or a designer uses to buy or design perfect fit clothes. As a result, DeepDraper significantly outperforms the state-of-the-art deep network-based approaches in terms of fitness and realism and generalizes well to the unseen style of the garments. In addition to that, DeepDraper is ~ 10 times smaller in size and ~ 23 times faster than the closest state-of-the-art method (TailorNet), which favors its use in real-time applications with less computational power. Despite being trained on the static poses of the TailorNet [32] dataset, DeepDraper generalizes well to unseen body shapes, poses, and garment styles and produces temporally coherent garment deformations on the pose sequences even from the unseen AMASS [25] dataset.
Development of a fluoroscopically guided robotic assistant for instrument placement in pelvic trauma surgery (2021)

<b>Purpose:</b> A method for fluoroscopic guidance of a robotic assistant is presented for instrument placement in pelvic trauma surgery. The solution uses fluoroscopic images acquired in standard clinical workflow and helps avoid repeat fluoroscopy commonly performed during implant guidance. <b>Approach:</b> Images acquired from a mobile C-arm are used to perform 3D-2D registration of both the patient (via patient CT) and the robot (via CAD model of a surgical instrument attached to its end effector, e.g; a drill guide), guiding the robot to target trajectories defined in the patient CT. The proposed approach avoids C-arm gantry motion, instead manipulating the robot to acquire disparate views of the instrument. Phantom and cadaver studies were performed to determine operating parameters and assess the accuracy of the proposed approach in aligning a standard drill guide instrument. <b>Results:</b> The proposed approach achieved average drill guide tip placement accuracy of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>1.57</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.47</mml:mn> <mml:mtext> </mml:mtext> <mml:mi>mm</mml:mi></mml:mrow> </mml:math> and angular alignment of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>0.35</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.32</mml:mn> <mml:mtext> </mml:mtext> <mml:mi>deg</mml:mi></mml:mrow> </mml:math> in phantom studies. The errors remained within 2 mm and 1 deg in cadaver experiments, comparable to the margins of errors provided by surgical trackers (but operating without the need for external tracking). <b>Conclusions:</b> By operating at a fixed fluoroscopic perspective and eliminating the need for encoded C-arm gantry movement, the proposed approach simplifies and expedites the registration of image-guided robotic assistants and can be used with simple, non-calibrated, non-encoded, and non-isocentric C-arm systems to accurately guide a robotic device in a manner that is compatible with the surgical workflow.
Enhanced Raw Image Capture and Deblurring (2022)

Camera motion blur is a common problem in low-light imaging applications. Over the year numerous algorithms have been developed to deblur the image and provide a visually pleasing capture of the sensed scene. Many of these algorithms require that the blur kernel is known a priori which limits their application in many real-world situations. Recently, inertial sensors have been utilized in an attempt to estimate a blur kernel that can then be incorporated into deblurring algorithms to provide improved results. However, the effectiveness of these algorithms has been limited by lack of access to unprocessed raw image data obtained directly from the image sensor. In this thesis, we build an digital imaging system for the acquisition of raw im- age data in conjunction with 3-axis acceleration data. From the acceleration data camera motion during image capture can be estimated to provide information about blurring of the sensed scene. This blur kernel is used in a maximum a posteriori esti- mation algorithm to deblur the raw image data. Experiments demonstrate that the accelerometer-based deblurring algorithm on raw image data can generate improved results.
CEACAM1 regulates TIM-3-mediated tolerance and exhaustion (2014)

CEACAM1 functions as a novel heterophilic ligand for TIM-3 and is necessary for TIM-3-mediated tolerance, which has marked consequences for inflammation, infection and cancer.
Reversible Doping and Photo Patterning of Polymer Nanowires (2020)

Abstract Recent development of dopant induced solubility control (DISC) patterning of polymer semiconductors has enabled direct‐write optical patterning of poly‐3‐hexylthiophene (P3HT) with diffraction limited resolution. Here, the optical DISC patterning technique to the most simple circuit element, a wire, is applied. Optical patterning of P3HT and P3HT doped with the molecular dopant 2,3,5,6‐tetrafluoro‐7,7,8,8‐tetracyanoquinodimethane (F4TCNQ) wires with dimensions of 20–70 nm thickness, 200–900 nm width, and 40 μm length is demonstrated. In addition, optical patterning of wire patterns like “L” bends and “T” junctions without changing the diameter or thickness of the wires at the junctions is demonstrated. The wires themselves show up to 0.034 S cm ‐1 conductance when sequentially doped. It is also demonstrated that a P3HT nanowire can be doped, de‐doped, and re‐doped from solution without changing the dimension of the wire. The combined abilities to optically pattern and reversibly dope a polymer semiconductor represents a full suite of patterning steps equivalent to photolithography for inorganic semiconductors.
Ada Mae (2017)

This is the story of Ada Grashow—a loving, gentle soul touched by a rare genetic condition, Phelan–McDermid syndrome (PMS). This chapter gives voice to the Grashow family’s journey to their happy ever after. It was during January 2015 that we had the pleasure of first meeting Ada Mae and her family, including Ada’s younger sister, Wilhelmina (Willa), and parents, Jon and Katie (See Figure 22.1). The family of four is a close-knit unit, sharing an infectious love with those around them. The lab instantly felt a strong attachment to the family, with time spent recalling stories from lands afar and playing “house.” One of these heartfelt moments was particularly striking, hitting a cord with our team. During one session, a member of our team, Caroline, sat quietly coloring with Willa. Caroline, who had recently returned from spending a holiday break with her family in Ireland—including sitting through multiple repeats of Disney’s latest hit, Frozen, with her 5-year-old niece—asked Willa if she had seen the film. After a brief pause, Willa stopped coloring. She responded that she had seen the film, and that her favorite princess was Elsa, before quickly returning her attention to the coloring task. Not providing the enthusiastic response to the mere mention of Frozen that many may be used to, Willa quietly went on to explain that it made her very sad. The story reminded her of Ada. To a young Willa, her sister Ada had been lost to her, paralleling the Frozen story line, but had never returned as Elsa had in the movie. The similarities were obvious to this young girl, and the film uniquely summarized the heartbreaking story of this family. Katie, overhearing the conversation from the lab room, confirmed that they had both watched the Disney hit together, struggling to hold back the tears and hugging each other close. Katie and Jon later explained that they have learned to avoid many mainstream TV shows and movies because the dramatic plots are too upsetting to be entertaining, given the family’s real-life experiences. Ada was 4½ years old when she became “frozen,” or regressed. This is their story.
O2‐12‐03: Transcranial Direct Current Stimulation to the Left Parietal Lobe Combined with Training Improves Naming and Digit Span in People with Dementia (2016)

Transcranial direct current stimulation (tDCS) has been used to treat a wide variety of ailments: e.g. Depression, Stroke, and Parkinson's disease. We examined how transcranial direct current stimulation (tDCS) could help improve naming abilities in people living with dementia (Alzheimer’s and frontotemporal). Eight participants, in a cross-over double-blind study, were trained on picture naming over a series of sessions that included either an initial 30 minutes of anodal (2 mA) tDCS stimulation to the parietal lobe (P3), or sham stimulation. Evaluation involved a set of naming and cognitive-based tasks before stimulation, on the final stimulation session, and two weeks post-stimulation. Training effects were examined by evaluating participants’ ability to name images from two lists matched for familiarity, but having only one of these lists trained during the stimulation sessions. We found participants receiving real anodal parietal tDCS stimulation improved twice as much as when these same participants received sham tDCS. Furthermore, these participants showed a small increase for untrained items and digit span when they received real stimulation, but a decrease when sham stimulation was received.
Applications of the 12 Principles of Green Chemistry in the Crop Protection Industry (2019)

This review discusses specific examples of the application of the 12 principles of green chemistry from the crop protection industry. Many of the examples are operated on a multiton scale. Although there are numerous examples of green chemistry in agrochemical manufacture, a consistent, holistic application of these principles is encouraged to minimize the environmental footprint and increase the safety of commercial synthetic routes to crop protection active ingredients.
Mutational Mapping and Modeling of the Binding Site for (S)-Citalopram in the Human Serotonin Transporter (2009)

The serotonin transporter (SERT) regulates extracellular levels of the neurotransmitter serotonin (5-hydroxytryptamine) in the brain by facilitating uptake of released 5-hydroxytryptamine into neuronal cells. SERT is the target for widely used antidepressant drugs, including imipramine, fluoxetine, and (S)-citalopram, which are competitive inhibitors of the transport function. Knowledge of the molecular details of the antidepressant binding sites in SERT has been limited due to lack of structural data on SERT. Here, we present a characterization of the (S)-citalopram binding pocket in human SERT (hSERT) using mutational and computational approaches. Comparative modeling and ligand docking reveal that (S)-citalopram fits into the hSERT substrate binding pocket, where (S)-citalopram can adopt a number of different binding orientations. We find, however, that only one of these binding modes is functionally relevant from studying the effects of 64 point mutations around the putative substrate binding site. The mutational mapping also identify novel hSERT residues that are crucial for (S)-citalopram binding. The model defines the molecular determinants for (S)-citalopram binding to hSERT and demonstrates that the antidepressant binding site overlaps with the substrate binding site.
Broad reactivity and enhanced potency of recombinant anti-EGFR × anti-CD3 bispecific antibody-armed activated T cells against solid tumours (2022)

<b>Introduction:</b> Bispecific antibody (BiAb)-armed activated T cells (BATs) comprise an adoptive T cell therapy platform for treating cancer. Arming activated T cells (ATC) with anti-CD3 x anti-tumour associated antigen (TAA) BiAbs converts ATC into non-major histocompatibility complex (MHC)-restricted anti-tumour cytotoxic T lymphocytes (CTLs). Binding of target antigens via the BiAb bridge enables specific anti-tumour cytotoxicity, Th1 cytokines release, and T cell proliferation. Clinical trials in breast, prostate, and pancreatic cancer using BATs armed with chemically heteroconjugated BiAbs demonstrated safety, feasibility, induction of anti-tumour immune responses and potential increases in overall survival (OS).<b>Objectives:</b> The primary objective of this study was to develop a recombinant BiAb that confers enhanced anti-tumour activity of BATs against a broad range of solid tumours.<b>Methods:</b> A recombinant anti-epidermal growth factor receptor (EGFR) x anti-CD3 (OKT3) BiAb (rEGFRBi) was designed and expressed in CHO cells, used to arm ATC (rEGFR-BATs), and tested for specific cytotoxicity against breast, pancreatic and prostate cancers and glioblastoma.<b>Results:</b> rEGFR-BATs exhibit remarkably enhanced specific cytotoxicity and T1 cytokine secretion against a wide range of solid tumour cell lines vs. their respective chemically-heteroconjugated BATs.<b>Conclusion:</b> rEGFR-BATs may provide a "universal" T cell therapy for treating a wide range of solid tumours. KEY MESSAGEA (Gly4Ser)6 linker between the variable light and heavy chains of an scFv fused to the N-terminus of a heavy chain antibody confers unexpected stability to the heavy chain fusion protein and supports the efficient expression of the bispecific antibody.Arming of activated T cells with the rEGFRBi greatly enhances the relative cytotoxicity and Th1 cytokine secretion of theT cells relative to a chemically heteroconjugated BiAbs.rEGFR-BATs are promising candidates for the treatment of a broad range of solid tumours.
CELLULAR UPTAKE AND EXCRETION OF ZINC TETRA-SULFOPHTHALOCYANINE (1989)

Cellular uptake and excretion of Zn-tetrasulfophthalocyanine (ZnTSPc) was determined by spectrophotometric analysis of the supernatant. After incubation time of 15, 30, 60, 1440 min. with ZnTSPc, cellular uptake was found to be 1.9 pico g per single Hela cell that corresponds to about 109 molecules of ZnTSPc localized in or on one cell. This indicates that cellular uptake rate of ZnTSPc is fast. Cellular excretion of ZnTSPc was observed after removal of this photosensitizer from the medium. Though 16 percent of ZnTSPc that was taken in or on cells was excreted after 72 hr., no significant differences in efficiency of Photodynamic effects on cell inactivation was observed.
Coherently driven non-classical light emission from a quantum dot (2007)

Narrow line-widths and the possibility of enhanced spontaneous emission via coupling to microcavities make semiconductor quantum dots ideal for harnessing coherent quantum phenomena at the single photon level. So far, however, all approaches have relied on incoherent pumping, which limits the desirable properties of the emission. In contrast, coherent excitation was recognized to be necessary for providing both improved photon indistinguishability and high efficiency, and offers the quantum control capabilities required for basic qubit manipulations. Here we achieve, for the first time, resonant and coherent excitation of a quantum dot with simultaneous collection of the non-classical photon emission. Second-order correlation measurements show the unique signature of a coherently-driven two-level quantum emitter: the photon statistics become oscillatory at high driving fields, reflecting the coherent evolution of the excitonic ground state of the quantum dot.
ChemInform Abstract: Broadly Applicable Z‐ and Diastereoselective Ring‐Opening/Cross‐Metathesis Catalyzed by a Dithiolate Ru Complex. (2014)

Abstract All the products are obtained with excellent (Z)‐selectivities.
XForms 2.0 (2012)

XForms is an XML markup for a new generation of forms and form-like applications on the Web. XForms is not a free-standing document type, but is integrated into other markup languages, such as [XHTML], [ODF] or [SVG]. An XForms-based application gathers and processes data using an architecture that separates presentation, purpose and content. The underlying data of a form is organized into instances. XForms allows processing of data to occur using three mechanisms: a declarative model composed of formulae for data calculations and constraints, data type and other property declarations, and data submission parameters a view layer composed of intent-based user interface controls an imperative controller for orchestrating data manipulations, interactions between the model and view layers, and data submissions. 

Thus, XForms accommodates form component reuse, fosters strong data type validation, eliminates unnecessary round-trips to the server, offers device independence and accessibility, and reduces the need for scripting. 

XForms 2.0 adds support for defining custom functions, variables, a pluggable expression language with extra functions (XPath 2.0), model-based switch and repeat, Attribute Value Templates, consuming and submitting JSON and CSV instance data, amongst other things.
CREATING CELLULAR MICROPATTERNS BY SWITCHING FOULING PROPERTIES OF ELECTROACTIVE ITO SURFACES (2008)

This paper describes a novel approach of forming micropatterned co-cultures using a combination of oxygen plasma ashing and electrochemical removal of poly(ethylene glycol) (PEG) silane from indium tin oxide (ITO) substrates. After assembling a layer of PEG silane on ITO, photolithography and oxygen plasma cleaning were used to form cell-adhesive domains within the non-fouling PEG silane layer. After patterning hepatocytes in these domains, the surrounding PEG silane layer was desorbed by applying negative voltage (-1.4 V vs. Ag/AgCl) to the underlying ITO substrate. This switched the fouling properties of the ITO substrate and allowed the adsorption of another cell type creating a micropatterned co-culture.
Percutaneous Ablation in the Kidney (2011)

Percutaneous ablation in the kidney is now performed as a standard therapeutic nephron-sparing option in patients who are poor candidates for resection. Its increasing use has been largely prompted by the rising incidental detection of renal cell carcinomas with cross-sectional imaging and the need to preserve renal function in patients with comorbid conditions, multiple renal cell carcinomas, and/or heritable renal cancer syndromes. Clinical studies to date indicate that radiofrequency ablation and cryoablation are effective therapies with acceptable short- to intermediate-term outcomes and with a low risk in the appropriate setting, with attention to pre-, peri-, and postprocedural detail. The results following percutaneous radiofrequency ablation and cryoablation in the treatment of renal cell carcinoma are reviewed in this article, including those of several larger scale studies of ablation of T1a tumors. Clinical and technical considerations unique to ablation in the kidney are presented, and potential complications are discussed.