gebhart/patrepeval huggingface dataset:
Proposal of three-dimensional phase contrast holographic microscopy: erratum (2008)

A part of the schematic in Fig. 1 was incorrect. The correct version is presented herein. ©2008 Optical Society of America OCIS codes: (180.6900) Three-dimensional microscopy; (180.5810) Scanning microscopy; (110.0180) Microscopy; (090.2880) Holographic interferometry; (110.4850) Optical transfer function. References and links 1. N. Fukutake and T. D. Milster, “Proposal of three-dimensional phase contrast holographic microscopy,” Opt. Express 15, 12662 (2007). A part of Fig. 1 in [1] was incorrect; it is corrected below. The scanning mirror in Fig. 1 of [1] is replaced with a double-sided mirror whose normal direction is also scanned twodimensionally. The propagation direction of the plane wave which illuminates the object is scanned by the obverse side of the double-sided scanning mirror. The 0-order light transmitted through the object is reflected by the reverse side of the scanning mirror, resulting in the identical direction of the 0-order light irrespective of the scanning mirror angle. Fig. 1. Schematic of the setup of the 3-D phase contrast holographic microscopy. BS: Beam splitter. 2 / λ : Half wave plate. 4 / λ : Quarter wave plate. PBS: Polarized beam splitter. #94643 $15.00 USD Received 7 Apr 2008; accepted 7 Apr 2008; published 11 Apr 2008 (C) 2008 OSA 14 April 2008 / Vol. 16, No. 8 / OPTICS EXPRESS 5964
Developing near-isogenic lines of IR64 introgressed with QTLs for deeper and thicker roots through marker-aided selection (1999)

A well-developed root system is an important trait contributing to drought resistance in rice. Preliminary work allowed us to map QTLs involved in the control of several root traits in a doubled-haploid population of rice derived from the cross IR64 x Azucena. We are now developing near-isogenic lines of IR64 introgressed with the major QTLs. Four segments on chromosomes 1, 2, 7, and 9 were initially targeted for single QTL selection. Four doubled-haploid lines with the proper allelic combination at the targeted segments and less than 50% Azucena alleles in the rest of the genome were chosen as donors. These lines were backcrossed on IR64 up to the BC3F1 generation and then selfed. Marker-aided selection for the target segments was performed from BC1F1 up to BC3F2. All he selected BC3F2 progenies carried the donor alleles for at least one target region. Plants carrying two target segments were also identified. Phenotypic variation for several nonarget traits was observed in the BC3F2 plants, suggesting the presence of genetic drag during introgression. A background survey of the rest of the genome indicated that the BC3F2 plants had a very small portion of Azucena alleles in the non-target regions, close to the expected ~3%. Crosses were made between BC3F2 plants carrying different target donor segments to remove possible genetic drag and pyramid different target QTLs.
Abstract PR006: Multi-modal single-cell profiling of sarcomas from archival tissue reveals mechanisms of resistance to immune checkpoint inhibitors (2022)

Abstract Single-cell genomics is an enabling technology that may inform the molecular underpinnings of drug response and resistance in patient biopsies. These methods are difficult to implement in the study of rare diseases such as sarcomas due to specimen requirements and technical limitations. Here, we evolved novel methods that we recently reported in melanoma (Wang, Fan, et al., bioRxiv, 2022) which enable single-nucleus RNA, T cell receptor (snRNA/TCR-seq), and pool-matched whole-genome sequencing (WGS) from archival frozen sarcoma tissue. This enabled profiling of 75,716 cells and 788 matched TCR clonotypes from six patients with intimal sarcoma (INS) and undifferentiated pleomorphic sarcoma (UPS), including two matched pair samples from pre/post-immune checkpoint inhibitor (ICI). Our analysis revealed substantial transcriptional cancer cell heterogeneity driven by varying copy number alterations (CNAs). In one patient with INS with a complete response to ICI followed by an isolated recurrence, we identified a rare cancer cell clone defined by CNA (confirmed with WGS) and resulting transcriptional outputs that pre-existed and emerged during resistance. Furthermore, in a UPS patient with intrinsic resistance to ICI, we find adequate T cell clonal expansion, activation, and differentiation, suggesting appropriate T cell response to ICI dampened by intrinsic mechanisms of ICI resistance within the cancer cells. Non-negative matrix factorization (NMF) analysis identified cell states associated with either intrinsic or adaptive resistance to ICI that was distinct from resistance to doxorubicin. These observations are consistent with those previously reported from sequential biopsies obtained from KEYNOTE-001 in metastatic melanoma (Wang, Fan, et al., bioRxiv, 2022), which also revealed emergence of pre-existing populations of resistant clones defined by their underlying aneuploidy patterns. Together, these results demonstrate feasibility of implementing single-cell genomics from archival tissue to study sarcoma and propel our understanding of drug resistance. Conceptually, this work suggests that large-scale CNAs may allow us to identify cell sub-populations associated with ICI resistance in sarcoma and in other diseases. Citation Format: Sminu Bose, Blake Caldwell, Amit Dipak Amin, Johannes Melms, Somnath Tagore, Matthew Ingham, Benjamin Izar, Gary K. Schwartz. Multi-modal single-cell profiling of sarcomas from archival tissue reveals mechanisms of resistance to immune checkpoint inhibitors [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR006.
Efficient Synthesis and Structural Characteristics of Zwitterionic Twisted π-Electron System Biaryls (2005)

A series of unconventional twisted pi-electron system molecules has been synthesized via Suzuki cross-coupling of two sterically hindered arenes. Crystallographic analysis of these molecules reveals a large ring-ring dihedral twist angle (87 degrees ) and a highly charge-separated zwitterionic ground state. An efficient conversion of phenols into aryl halides is also reported. [reaction: see text]
Detection of NP, N3 and N7 antibodies to avian influenza virus by indirect ELISA using yeast-expressed antigens (2009)

The study demonstrates the expression of the NP, N3, and N7 proteins of AIV in yeast (S. cerevisiae) and their application in developing an indirect ELISA for detecting NP, N3 and N7 antibodies from AIV-infected chicken sera. The described indirect ELISAs are rapid, sensitive, specific and can be used as promising tests during serological surveillance.
Tunable liquid crystal phase shifter for microwave frequencies (2009)

A tunable phase shifter using liquid crystal (LC) is presented. The device is fabricated in a fashion similar to LC displays which makes fabrication very simple compared, for example, to MEMS approaches. At the targeted operation frequency of 20 GHz the device offers a performance of above 60° differential phase shift per dB insertion loss and a minimum tuning speed of 340 ms.
Sensitive Detection of Bacillus anthracis Spores by Immunocapture and Liquid Chromatography–Tandem Mass Spectrometry (2011)

Bacillus anthracis is one of the most dangerous agents of the bioterrorism threat. We present here a sensitive immuno-liquid chromatography-tandem mass spectrometry (immuno-LC-MS/MS) approach to spore detection in complex environmental samples. It is based on the combined specificity and sensitivity of two techniques: immunocapture and targeted mass spectrometry. The immunocapture step, realized directly on the intact spores, is essential for their selective isolation and concentration from complex environmental samples. After parallel trypsin and Glu-C digestions, proteotypic peptides corresponding to small acid-soluble spore protein-B (SASP-B) are specifically monitored in the multiple reaction monitoring (MRM) mass spectrometry mode. Peptide ratio is carefully monitored and provides an additional level of specificity, which is shown to be highly useful for distinguishing closely related samples and avoiding false-positive/negative results. Sensitivity at the level of the infectious dose is demonstrated, with limits of detection of 7 × 10(3) spores/mL of milk or 10 mg of soil. This mass spectrometry approach is thus complementary to polymerase chain reaction (PCR) techniques.
Fine-grained end-to-end network model via vector quantization and hidden Markov processes (2013)

We study and compare modeling an end-to-end network by conventional, bivariate, and exponential observation hidden Markov processes. Furthermore, effects of μ-law, Lindle-Boyde-Gray, and uniform quantization approaches on the modeling granularity is explored. We performed experiments using synthetic representative data from a traffic-modeler autoregressive modular process and the Network Simulator software as well as over-the-Internet experiments with real data to contrast the fidelity produced from each model. Comparing statistical signatures of the model-generated data with those of the training sequence indicates that accompanying Lindle-Boyde-Gray quantization with conventional or bivariate hidden Markov processes significantly improves the modeling fidelity.
Neuroprotection of the Perinatal Brain by Early Information of Cerebral Oxygenation and Perfusion Patterns (2021)

Abnormal patterns of cerebral perfusion/oxygenation are associated with neuronal damage. In preterm neonates, hypoxemia, hypo-/hypercapnia and lack of cerebral autoregulation are related to peri-intraventricular hemorrhages and white matter injury. Reperfusion damage after perinatal hypoxic ischemia in term neonates seems related with cerebral hyperoxygenation. Since biological tissue is transparent for near infrared (NIR) light, NIR-spectroscopy (NIRS) is a noninvasive bedside tool to monitor brain oxygenation and perfusion. This review focuses on early assessment and guiding abnormal cerebral oxygenation/perfusion patterns to possibly reduce brain injury. In term infants, early patterns of brain oxygenation helps to decide whether or not therapy (hypothermia) and add-on therapies should be considered. Further NIRS-related technical advances such as the use of (functional) NIRS allowing simultaneous estimation and integrating of heart rate, respiration rate and monitoring cerebral autoregulation will be discussed.
&lt;title&gt;Flexible design and implementation of an application programming interface for asynchronous transfer mode&lt;/title&gt; (1997)

Asynchronous transfer mode (ATM) network is one the most promising networks which are scalable in turn of bandwidth and distance. Moreover, bandwidth reservation and quality of service guarantees make ATM attractive to deliver multimedia information in real-time. Existing protocol suites fail to give access to those characteristics. therefore, applications demand an ATM application programming interface (API) forum has produced a semantics document which is independent of system platforms. This paper covers a special syntax mapping of the ATM API services on top of X/open transport interface (XTI) which is able to give applications access directly to the special quality and traffic services of an ATM network. A particular realization of the API on XTI environment is proposed and implemented on the MacOS networking platform. It provides a flexible and modular design of the ATM networking.
Damping and cushioning characteristics of Polyjet 3D printed photopolymer with Kelvin model (2020)

This study extends previous research on the measurement of a 3D printed photopolymer’s quasi-static cushion properties, to include cushion and damping properties due to impact loading. In order to develop analytical packaging models of 3D printed materials, it is essential to know how energy induced by shipping and handling is dissipated through damping. Compared to the cushion curve, investigating how damping influences packaging design is relatively unfamiliar to the packaging practitioner. This study uses experimentally derived hysteresis loops, from platen impact and quasi-static compression tests, to estimate specific damping capacities for 3D printed photopolymer. This study found that the “sticky” rubber like 3D printed photopolymers, based on a repeating pattern of Kelvin cells, were able to dissipate close to 100% of the input energy in platen impact tests and still return to their original dimensions after impact. In addition, this study shows that the specific damping capacity of the 3D printed structure increases significantly with strain rate.
Cyclooctatetraenide-Based Single-Ion MagnetsFeaturing Bulky Cyclopentadienyl Ligand (2022)

We report a family of organometallic rare-earth complexes with the general formula (COT)M(Cpttt) (where (COT)2– = cyclooctatetraenide, (Cpttt)– = 1,2,4-tri(tert-butyl)cyclopentadienide, M = Y(III), Nd(III), Dy(III) and Er(III)). Similarly to the prototypical Er(III) analog featuring pentamethylcyclopentadienyl ligand (Cp*)–, (COT)Er(Cpttt) behaves as a single-ion magnet. However, the introduction of the sterically demanding (Cpttt)– imposes geometric constraints that lead to a streamlined magnetic relaxation behavior compared to the (Cp*)– containing complexes. Consequently, (COT)Er(Cpttt) can be viewed as a model representative of this organometallic single-ion magnet architecture. In addition, we demonstrate that the increased steric profile associated with the (Cpttt)– ligand permits preparation, structural characterization and interrogation of magnetic properties of the early-lanthanide complex, (COT)Nd(Cpttt). Such a mononuclear derivative could not be obtained when a (Cp*)– ligand was employed, a testament to larger ionic radius of this early lanthanide ion.
Supplementary Figure 3 from Demonstration of a Genetic Therapeutic Index for Tumors Expressing Oncogenic &lt;i&gt;BRAF&lt;/i&gt; by the Kinase Inhibitor SB-590885 (2023)

Supplementary Figure 3 from Demonstration of a Genetic Therapeutic Index for Tumors Expressing Oncogenic &lt;i&gt;BRAF&lt;/i&gt; by the Kinase Inhibitor SB-590885
CD19 Directed Chimeric Antigen Receptor T Cell Therapy in Acute Lymphoblastic Leukemia: A Systematic Review and Meta-Analysis (2019)

IntroductionChimeric antigen receptor (CAR) T-cells targeting CD19 have led to complete response (CR) rates of 70-90% in children and adults with refractory/relapsed B-cell acute lymphoblastic leukemia (ALL), which led to their FDA approval in 2017. However, different constructs have been used and the response rates vary among different studies. Toxicities in the form of cytokine release syndrome (CRS) and neurotoxicity remain a challenge. We conducted a systematic review and meta-analysis of all published and presented trials of anti-CD19 CAR T-cells in relapsed/refractory ALL.Objectives1) To determine the efficacy of anti-CD19 CAR T-cells in ALL. 2) To describe the toxicities of anti-CD19 CAR T-cells in ALL. 3) To examine differences in efficacy and toxicity by age groups and construct type.MethodsWe searched MEDLINE and EMBASE and included studies that reported raw data on the outcomes of adults and children that were treated with anti-CD19 CAR T-cells for ALL. The random effects model was used to derive estimates of complete response (CR) and progression-free survival (PFS) at 1 year and toxicities. Secondary outcome was minimal residual disease (MRD) at 1 year. We planned subgroup analysis based on age (adults vs. children) and construct type.ResultsOf 1,139 potentially relevant references, 18 noncomparative trials were included with a total of 573 patients (309 adults and 264 children). Pooled CR was comparable between adults [84% (95 CI 80-86%)] and children [83% (95 CI 79-88%)], but varied by construct [86% (95 CI 82-90%) for 41BB co-stimulated CART cells vs 74% (95 CI 68-81%) for CD28 co-stimulated CART cells vs 86% (95 CI 80-91%) for fourth generation CART cells]. Pooled 1-year PFS was comparable for adults and children [53% (95 CI 31-74%) vs 56% (95 CI 50-65%)].CRS rates were comparable among adults and children [76% (95 CI 71-81%) vs 72% (95% CI 68-77%)]. CRS was lower in CD28 compared to other constructs [47% (95 CI 41-53%) in CD28 vs 86% (95 CI 82-91%) in 41BB vs 76% (95 CI 69-83%) in fourth generation]. Neurotoxicity occurred more commonly in adults [44% (95 CI 35-54%) vs 17% (95 CI 12-22%)] and in those treated with 41BB compared to those treated with CD28 [34% (95 CI 27-40%) vs 14% (95% CI 9-20%)].Pooled MRD negativity at 1 year was 77% (95 CI 71-82%) in adults and 82% (95 CI 77-87%) in children. CD28 construct led to lower MRD negativity [62% (95 CI 54-70%) vs 85% (95 CI 81-89%) in 41BB vs 81% (95 CI 69-93%) in fourth generation]. These data are summarized in Figure 1.ConclusionsPooled 1-year CR was 84%, pooled 1-year PFS was 57% and the efficacy of CAR T-cell therapy was comparable between adults and children. Analysis by construct type revealed differences in the efficacy and toxicity between different constructs with CD28 leading to lower efficacy and toxicity. This is the first study to systemically analyze the outcomes of anti-CD19 CAR T-cell therapy in ALL.
Quasi-cyclic LDPC codes for fast encoding (2005)

In this correspondence we present a special class of quasi-cyclic low-density parity-check (QC-LDPC) codes, called block-type LDPC (B-LDPC) codes, which have an efficient encoding algorithm due to the simple structure of their parity-check matrices. Since the parity-check matrix of a QC-LDPC code consists of circulant permutation matrices or the zero matrix, the required memory for storing it can be significantly reduced, as compared with randomly constructed LDPC codes. We show that the girth of a QC-LDPC code is upper-bounded by a certain number which is determined by the positions of circulant permutation matrices. The B-LDPC codes are constructed as irregular QC-LDPC codes with parity-check matrices of an almost lower triangular form so that they have an efficient encoding algorithm, good noise threshold, and low error floor. Their encoding complexity is linearly scaled regardless of the size of circulant permutation matrices.
The effects on hematopoiesis of recombinant stem cell factor (ligand for c-kit) administered in vivo to mice either alone or in combination with granulocyte colony-stimulating factor (1991)

Stem cell factor (SCF) is the ligand for the receptor encoded by the c-kit proto-oncogene. Mutations of either c-kit or the SCF gene are responsible for the defects of W and SI mutant mice, which both suffer a macrocytic anemia, the former associated with defective stem cells and the latter with a defective hematopoietic microenvironment. PEGylated recombinant rat SCF was administered to normal or splenectomized mice for up to 21 days. SCF was found to be a modest stimulator of peripheral blood neutrophil numbers in both groups of animals. The peak in neutrophil numbers was higher and occurred earlier in splenectomized mice. Bone marrow and spleen cellularity changed little during treatment but the content of interleukin-3-responsive progenitor cells and spleen colony-forming cells (CFU-S) reached very high levels, particularly in the spleen. Using recombinant human granulocyte colony-stimulating factor (rhG-CSF), we have shown that SCF induces a greater than additive increase in both blood neutrophils and blood-borne CFU-S. This synergy was seen throughout the dose range and may indicate a clinical role for SCF either alone or in augmenting the activity of G-CSF upon blood neutrophils and transplantable stem cells.
AC Loss of Superconducting Strands at High frequencies, and the impact for Harmonic Contributions (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-4473.vid Superconducting windings are enabling for the development of the highest power density motors and generators for aircraft use. It is presently estimated that motors with normal conducting windings can reach a future limit of at best 20 kW/kg. On the other hand, superconducting windings are estimated to be able to produce more than double this, perhaps 45 kW/kg. While superconducting wires can carry high currents and do not have ohmic losses, they have other kinds of loss with AC excitation. These loss components; hysteretic, eddy current, and coupling loss predominantly, have interesting functional dependencies. Much of the work on AC loss in superconductors has been performed at lower frequencies, but higher frequencies are of interest for electric aircraft motors, particular with respect to harmonics, which can be high frequency (up to 10s of kHz) but are typically low amplitude. In order to properly estimate the losses for these harmonics, in this work we take into account the effects of the characteristic frequency fc1 as well as the skin depth frequency fc2; a skin depth frequency for the outer shell, fcs is also considered. The critical frequencies for a few round superconducting multifilamentary conductor variants are then considered, including several MgB2 strands and one Bi2212-type strand. The functional dependence of the losses are then considered in the high frequency regime, and the effect of this on harmonic loss components is considered.
Epidemiological investigations of human rabies in China (2009)

In recent years, rabies is reemerging and becoming a major public-health problem in China. Our analysis showed that unsuccessful control of dog rabies and inadequate PEP of patients were the main factors leading to the high incidence of human rabies in China, then there are following suggestions: (1) Strict control of free-ranging dogs and mandatory rabies vaccination should be enforced. (2)Establishing national animal rabies surveillance network is imperative. (3) PEP should be decided to initiate or withhold according to postmortem diagnosis of the biting animal. (4) The cost of PEP should be decreased or free, especially in rural areas. (5)Education of the public and health care staff should be enhanced.
CMA-ES-Rosetta: Blackbox optimization algorithm traverses rugged peptide docking energy landscapes (2022)

Abstract Energy minimization is necessary for virtually all modeling and design tasks and involves traversing extremely rugged energy landscapes. Although the gradient descent based minimization routines in Rosetta have fast runtimes, due to these rugged landscapes, minimization often converges into high-energy local minima. Alternative numerical optimization techniques, such as evolution strategies, are more robust to rugged landscapes and have been shown to be highly successful on a diverse set of problems. Here we explore the Covariance Matrix Adaptation Evolution Strategy (CMA-ES), a state-of-the-art derivative-free optimization algorithm, as a complementary approach to the default minimizer in Rosetta. We used a benchmark of 26 peptides, from the FlexPepDock Benchmark, to assess the performance of three algorithms in Rosetta, specifically, CMA-ES, Rosetta’s default minimizer, and a Monte Carlo protocol of small backbone perturbations. We test the algorithms’ performance on their ability to dock an idealized peptide to a series of hotspots residues (i.e. constraints) along a native peptide. Of the three methods, CMA-ES was able to find the lowest energy conformation for 23 out of 26 benchmark peptides. The application of CMA-ES allows for an alternative optimization method for macromolecular modeling problems with rough energy landscapes.