gebhart/patrepeval huggingface dataset:
Out-of-distribution Prediction with Invariant Risk Minimization: The Limitation and An Effective Fix (2021)

This work considers the out-of-distribution (OOD) prediction problem where (1)~the training data are from multiple domains and (2)~the test domain is unseen in the training. DNNs fail in OOD prediction because they are prone to pick up spurious correlations. Recently, Invariant Risk Minimization (IRM) is proposed to address this issue. Its effectiveness has been demonstrated in the colored MNIST experiment. Nevertheless, we find that the performance of IRM can be dramatically degraded under \emph{strong $Λ$ spuriousness} -- when the spurious correlation between the spurious features and the class label is strong due to the strong causal influence of their common cause, the domain label, on both of them (see Fig. 1). In this work, we try to answer the questions: why does IRM fail in the aforementioned setting? Why does IRM work for the original colored MNIST dataset? How can we fix this problem of IRM? Then, we propose a simple and effective approach to fix the problem of IRM. We combine IRM with conditional distribution matching to avoid a specific type of spurious correlation under strong $Λ$ spuriousness. Empirically, we design a series of semi synthetic datasets -- the colored MNIST plus, which exposes the problems of IRM and demonstrates the efficacy of the proposed method.
AsMA Medical Guidelines for Air Travel: Reported In-Flight Medical Events and Death (2015)

Medical Guidelines for Airline Travel provide information that enables healthcare providers to properly advise patients who plan to travel by air. Although there are no publicly available databases providing information on the number of in-flight medical emergencies, the few studies published in the literature indicate that they are uncommon. Minor illnesses such as near-fainting, dizziness, and hyperventilation occur more frequently. However, serious illnesses, such as seizures and myocardial infarction, also occur. In-flight deaths are also rare.
Transformation of Bicyclic Ketal Compound to 1,2-Cyclopentanediol via 1,5-Diketone (1992)

New method for preparing cyclopentanediol from bicyclic ketal is described. Bicyclic ketal is cleaved to give 1,5-diketone, which is then reductively coupled intramolecularly to yield 1,2-cyclopentanediol. A solution of bicyclic ketal (1a) in methylene chloride was treated with aluminum chloride(2 eq.)-sodium iodide(l.5 eq.) at ambient temperature for 3 h to give the 1,5-diketone (2a) in 71% yield after basic work-up followed by short path column chromatography. A solution of the 1,5-diketone (2a) in THF was reacted with titanium tetrachloride(6 eq.)-Mg(Hg)(0.3 eq.) at for 4 h to give the 1,2-cyclopentanediol (3a) in 75% yield after basic work-up followed by short path column chromatography.
A Cluster of Epoetin-Associated Pure Red Cell Aplasia: Clinical Features and the Possible Association of HLA-DRB1*12:02 (2016)

Antibody-mediated pure red cell aplasia is a rare but serious complication in chronic kidney disease patients receiving recombinant human erythropoietin (r-HuEpo). Between April 2012 and May 2013, eight such cases were reported in our institution. Their clinical features were reviewed and their HLA alleles were compared with those of healthy controls. All patients were exposed to epoetin alfa (Eprex<sup>®</sup>) with polysorbate-80 as stabilizer via subcutaneous route with a mean age of 61.9 years and mean exposure of 11.2 months of r-HuEpo before loss of efficacy. 87.5% of the cases were male and Chinese and received immunosuppression as treatment for pure red cell aplasia. All three of the successfully treated patients are alive compared with only 40% of the transfusion-dependent patients. DRB1*12:02 was more frequently expressed among the cases than healthy controls suggesting a plausible molecular link.
Advances in Biopreservation (2006)

Moving rapidly from science fiction to science fact, cryopreservation is an integral part of many research, development, and production processes in industry and academia. The preservation sciences have emerged as an interdisciplinary platform that incorporates the fundamentals of cell and molecular biology, and bioengineering, with the classic met
A single-chip CMOS Bluetooth transceiver with 1.5MHz IF and direct modulation transmitter (2003)

A single-chip Bluetooth transceiver in 0.18/spl mu/m CMOS integrates a direct VCO modulation transmitter and 1.5MHz-IF receiver to reduce power consumption and cost. The receiver achieves a sensitivity of -77dBm and transmitting power of +4dBm.
Interaction of Shc with the ζ Chain of the T Cell Receptor Upon T Cell Activation (1993)

The shc oncogene product is tyrosine-phosphorylated by Src family kinases and after its phosphorylation interacts with the adapter protein Grb2 (growth factor receptor-bound protein 2). In turn, Grb2 interacts with the guanine nucleotide exchange factor for Ras, mSOS. Because several Src family kinases participate in T cell activation and Shc functions upstream of Ras, the role of Shc in T cell signaling was examined. Shc was phosphorylated on tyrosine after activation through the T cell receptor (TCR), and subsequently interacted with Grb2 and mSOS. The Src homology region 2 (SH2) domain of Shc directly interacted with the tyrosine-phosphorylated zeta chain of the TCR. Thus, Shc may couple TCR activation to the Ras signaling pathway.
Kinetics versus Charge Separation: Improving the Activity of Stoichiometric and Non-Stoichiometric Hematite Photoanodes Using a Molecular Iridium Water Oxidation Catalyst (2016)

Oxygen-deficient iron oxide thin films, which have recently been shown to be highly active for photoelectrochemical water oxidation, were surface-functionalized with a monolayer of a molecular iridium water oxidation cocatalyst. The iridium catalyst was found to dramatically improve the kinetics of the water oxidation reaction at both stoichiometric and nonstoichiometric α-Fe2O3-x surfaces. This was found to be the case in both the dark and in the light as evidenced by cyclic voltammetry, Tafel analysis, and electrochemical impedance spectroscopy (EIS). Oxygen evolution measurements under working conditions confirmed high Faradaic efficiencies of 69–100% and good stability over 22 h of operation for the functionalized electrodes. The resulting ∼200–300 mV shift in onset potential for the iridium-functionalized sample was attributed to improved interfacial charge transfer and oxygen evolution kinetics. Mott–Schottky plots revealed that there was no shift in flat-band potential or change in donor density following functionalization with the catalyst. The effect of the catalyst on thermodynamics and Fermi level pinning was also found to be negligible, as evidenced by open-circuit potential measurements. Finally, transient photocurrent measurements revealed that the tethered molecular catalyst did improve charge separation and increase charge density at the surface of the photoanodes, but only at high applied biases and only for the nonstoichiometric oxygen-deficient iron oxide films. These results demonstrate how molecular catalysts can be integrated with semiconductors to yield cooperative effects for photoelectrochemical water oxidation.
Efficacies of Fluconazole, Caspofungin, and Amphotericin B inCandida glabrata-Infected p47phox−/−Knockout Mice (2002)

Candida glabrata is the second leading cause of adult candidemia, resulting in high mortality. Amphotericin B is considered the treatment of choice, while the efficacy of fluconazole is controversial and caspofungin efficacy is unknown. To ascertain drug efficacy in vivo, the utility of a murine model of C. glabrata infection was investigated. C. glabrata was found to cause progressive, lethal infection when injected intravenously into C57BL/6 mice with reduced oxidative microbicidal capacity due to knockout of the p47(phox) gene. Spleen and kidney organ CFU counts were determined in groups of mice 2 days after the mice completed 6 days of daily intraperitoneal drug treatment, which began on the day of infection. Daily injections of fluconazole at 80 mg/kg did not reduce spleen or kidney CFU counts after infection with C. glabrata strains having in vitro fluconazole MICs of 2, 32, or 256 microg/ml compared to saline-treated controls. However, this fluconazole regimen reduced spleen CFU counts in mice infected with Candida albicans, an infection that is known to be responsive to fluconazole. Caspofungin at 5 mg/kg and amphotericin B at 5 mg/kg were both effective in reducing fungal burden in spleens and kidneys of C. glabrata-infected mice. Ten mice treated for 6 days with caspofungin at 1 mg/kg survived for 15 days, though all 10 saline-injected mice died or were so ill that they had to be sacrificed by 96 h postinfection. This murine model provided evidence of the efficacy of amphotericin B and caspofungin but not of fluconazole against C. glabrata infection.
Epidermal growth factor receptor (EGFR)-targeted immunoliposomes mediate specific and efficient drug delivery to EGFR- and EGFRvIII-overexpressing tumor cells (2004)

We hypothesized that immunoliposomes (ILs) that target epidermal growth factor receptor (EGFR) and/or its truncated variant EGFRvIII can be constructed to provide efficient intracellular drug delivery in tumor cells overexpressing these receptors. Monoclonal antibody fragments included Fab' fragments derived from C225, which binds both EGFR and EGFRvIII, or novel anti-EGFR scFv C10, which binds EGFR only. Monoclonal antibody fragments were covalently linked to liposomes containing various reporters or drugs. ILs were evaluated for specific binding, internalization, and cytotoxicity in EGFR/EGFRvIII-overexpressing cell lines in vitro. Flow cytometry and fluorescence microscopy showed that EGFR-targeted ILs, but not nontargeted liposomes or irrelevant ILs, were efficiently bound and internalized by EGFR-overexpressing cells, including glioma cells (U-87), carcinoma cells (A-431 and MDA-MB-468), and EGFRvIII stable transfectants (NR-6M). Furthermore, EGFR-targeted ILs did not bind to non-EGFR-overexpressing cells (MCF-7 and parental NR-6). ILs showed 3 orders of magnitude greater accumulation in NR-6-EGFRvIII stable transfectants versus parental NR-6 cells. Quantitative internalization studies indicated binding of EGFR-targeted ILs to target cells within 5 min, followed by intracellular accumulation beginning at 15 min; total uptake reached approximately 13,000 ILs/cell. ILs were used to deliver cytotoxic drugs doxorubicin, vinorelbine, or methotrexate to EGFR/EGFRvIII-overexpressing target cells in vitro. In each case, the IL agent was significantly more cytotoxic than the corresponding nontargeted liposomal drug in target cells, whereas it was equivalent in cells lacking EGFR/EGFRvIII overexpression. We conclude that EGFR-targeted ILs provide efficient and targeted delivery of anticancer drugs in cells overexpressing EGFR or EGFRvIII.
Data from Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System (2023)

&lt;div&gt;Abstract&lt;p&gt;The neuroendocrine carcinoma of the gastrointestinal system (GIS-NEC) is a rare but highly malignant neoplasm. We analyzed 115 cases using whole-genome/exome sequencing, transcriptome sequencing, DNA methylation assays, and/or ATAC-seq and found GIS-NECs to be genetically distinct from neuroendocrine tumors (GIS-NET) in the same location. Clear genomic differences were also evident between pancreatic NECs (Panc-NEC) and nonpancreatic GIS-NECs (Nonpanc-NEC). Panc-NECs could be classified into two subgroups (i.e., “ductal-type” and “acinar-type”) based on genomic features. Alterations in &lt;i&gt;TP53&lt;/i&gt; and &lt;i&gt;RB1&lt;/i&gt; proved common in GIS-NECs, and most Nonpanc-NECs with intact RB1 demonstrated mutually exclusive amplification of &lt;i&gt;CCNE1&lt;/i&gt; or &lt;i&gt;MYC&lt;/i&gt;. Alterations of the Notch gene family were characteristic of Nonpanc-NECs. Transcription factors for neuroendocrine differentiation, especially the &lt;i&gt;SOX2&lt;/i&gt; gene, appeared overexpressed in most GIS-NECs due to hypermethylation of the promoter region. This first comprehensive study of genomic alterations in GIS-NECs uncovered several key biological processes underlying genesis of this very lethal form of cancer.&lt;/p&gt;Significance:&lt;p&gt;GIS-NECs are genetically distinct from GIS-NETs. GIS-NECs arising in different organs show similar histopathologic features and share some genomic features, but considerable differences exist between Panc-NECs and Nonpanc-NECs. In addition, Panc-NECs could be classified into two subgroups (i.e., “ductal-type” and “acinar-type”) based on genomic and epigenomic features.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 587&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
High-throughput and versatile design for multi-layer coating deposition using lab automation through Arduino-controlled devices (2021)

Laboratory and experimental scale manufacturing processes are limited by human error (e.g., poor control over motion and personal subjectivity), especially under fatiguing conditions involving precise, repetitive operations, incurring compounding errors. Commercial layer-by-layer (LbL) automation devices are prohibitively high-priced (especially for academic institutions) with limited flexibility in form factor and potentially software-associated constraints/limitations. In this work, a novel automated multi-beaker dip coater was fabricated to facilitate nano cerium oxide/polymer coatings via an LbL dip coating process and the synthesis of nano ceria films via a novel successive ionic layer adsorption and reaction method on a glass substrate. Automation of tasks, such as those mediating the detailed procedures, is essential in producing highly reproducible, consistent products/materials as well as in reducing the time commitments for laboratory researchers. Herein, we detail the construction of a relatively large, yet inexpensive, LbL coating instrument that can operate over 90 cm in the horizontal axis, allowing, for example, up to eight 200 ml beakers with accompanying stir plates. The instrument is operated by simple "off-the-shelf" electronics to control the path and timing of the samples with open-source software while providing precision at ±0.01 mm. Furthermore, 3D-printed components were used to maximize the number of substrates that could be coated simultaneously, further improving the sample production rate and reducing waste. Further possibilities for automation beyond the detailed device are provided and discussed, including software interfaces, physical control methods, and sensors for data collection/analysis or for triggers of automated tasks.
INFLUENCE PROFILE OF WASTEWATER CHAIN IN AMSTERDAM: TOWARDS RESILIENT SYSTEM FOR PHOSPHORUS RECOVERY & VALORISATION (2018)

The wastewater system of Amsterdam offers an opportunity to recover phosphorus, and contribute to circular economy. However, it remains unclear where to intervene in system to maximize recovery and valorisation in a resilient and feasible way. The Design Structure Matrix method was tested to define the system architecture from Food-Water-Energy nexus perspective. Physical, phosphorus, and ownership dependencies between Infrastructure, Stakeholder, Resource and Cleantech domains (elements) of the wastewater system in Amsterdam are analyzed in a Multi-Domain Matrix model. Change Propagation Indicator quantified critical elements, and emergent changes. An Influence Profile unveiled four levels of system leverage: household, neighborhood, city-block, region. The stakeholders can engage into optimizations at each level, to generate individual and shared benefits. Hybrid infrastructure, plug&play solutions and modular approach to cleantech will harness up to 100% of phosphorus available. The method proved to be an effective tool for analysing complexity and engineering resilient solutions for the circular economy.
Tip-enhanced strong coupling spectroscopy, imaging, and control of a\n single quantum emitter (2019)

Optical cavities can enhance and control light-matter interactions. This has\nrecently been extended to the nanoscale, and with single emitter strong\ncoupling regime even at room temperature using plasmonic nano-cavities with\ndeep sub-diffraction-limited mode volumes. However, with emitters in static\nnano-cavities, this limits the ability to tune coupling strength or to couple\ndifferent emitters to the same cavity. Here, we present tip-enhanced strong\ncoupling (TESC) spectroscopy, imaging, and control. Based on a nano-cavity\nformed between a scanning plasmonic antenna-tip and the substrate, by\nreversibly and dynamically addressing single quantum dots (QDs) we observe mode\nsplitting &gt; 160 meV and anticrossing over a detuning range of ~100 meV, and\nwith sub-nm precision control over the mode volume in the ~1000 nm^3 regime.\nOur approach, as a new paradigm of nano-cavity quantum-electrodynamics\nnear-field microscopy to induce, probe, and control single-emitter plasmon\nhybrid quantum states, opens new pathways from opto-electronics to quantum\ninformation science.\n
Exploring the gap between dynamic and steady-state models of metabolism (2010)

Integration of different kinds of biological networks, is within the holistic approach of Systems Biology. However, looking at metabolic networks only, one already finds a separation between dynamic [2] and steady-state [3] models of metabolism. This work reviews the differences between both modeling approaches and explores the gap between them. Common properties of both kind of models are studied in detail, using as case study the central carbon metabolism of E. coli. Steadystate models are underdetermined and define a space of possible solutions, the so-called flux cone [4]. On the other hand, the kinetic properties of dynamic models define a specific flux distribution inside this space of solutions. We explore how this particular solution changes in function of initial conditions and the different kinetic parameters. Due to changes in experimental conditions and experimental measurement error, these parameters can vary in a wide range, changing the flux distribution around its original value within a kinetically feasible solution space. We perform Monte Carlo sampling [5] to analyze the solution space of both the dynamic and steady-state models. We estimate the volume of the kinetically feasible solution space under different restrictions and find it to be considerably smaller than the volume of the steady-state flux cone. -rherefore, it is possible to cope with the lack and uncertainty in experimental data by defining refined solution spaces that can be used in constraint-based methods [1] such as Flux Balance Analysis.
Color electronic paper (2015)

AccessScience is an authoritative and dynamic online resource that contains incisively written, high-quality educational material covering all major scientific disciplines. An acclaimed gateway to scientific knowledge, AccessScience is continually expanding the ways it can demonstrate and explain core, trustworthy scientific information that inspires and guides users to deeper knowledge.
BIOM-44. MAGNETIC RESONANCE IMAGING MAPPING OF BRAIN TUMOR BURDEN TO EVALUATE RESPONSE TO PULSED LOW-DOSE-RATE RADIOTHERAPY FOLLOWING RESECTION OF GLIOBLASTOMA MULTIFORME: A 4-PATIENT CASE SERIES (2022)

Abstract BACKGROUND Pulsed low-dose-rate radiotherapy (pLDR) is an accepted reirradiation technique for recurrent glioma, but its upfront use, concurrent with temozolomide (TMZ) following resection of high-grade glioma is currently under investigation. Evaluating the response to upfront radiation can be challenging and there is limited data on expected rates of pseudoprogression with pLDR. Standard magnetic resonance imaging (MRI) has limitations in differentiating pseudoprogression from tumor progression, sometimes necessitating surgery for pathologic confirmation. Advanced MRI can be used to create fractional tumor burden (FTB) maps that spatially distinguish active tumor from treatment-related effect (pseudoprogression), perhaps providing a more reliable imaging biomarker in the absence of additional surgery. METHODS We performed a retrospective chart review to report the responses of four patients with glioblastoma to upfront pLDR and TMZ following resection. Each patient received advanced surveillance MRI and redo surgery. Tumor pathology included IDH-wild type (n = 4) and O6-methylguanine-DNA methyltransferase (MGMT) methylated (n = 1) tumors. RESULTS The median age of patients was 57.5 years (range 55-60 years) and all were male. One patient experienced mortality and another was transitioned to hospice. In all four cases, there were concerns of tumor progression in postcontrast MRI. Pathologic diagnosis revealed either treatment effect (n = 2) or tumor (n = 2). FTB maps were predominantly indicative of lesion volumes being comprised of treatment effect (n = 3) and tumor (n = 1). From the three FTB maps in the former category, the median fraction of the enhancing tumor volume comprised of vascular tumor was 6.4% (range 1.8-6.8%). CONCLUSION This case series provides insight into response to upfront pLDR and TMZ following resection of glioblastoma and demonstrates the capacity for FTB mapping to spatially distinguish tumor progression from treatment effect in this patient population.
IIIV/SOI Heterogeneous Integration of Optoelectronic Devices (2008)

Based on a microdisk laser (MDL) structure by a IIIV/SOI heterogeneous integration platform, we introduce mutiwavelength laser sources, optical modulators, wavelength converters potentially for on-chip optical interconnect.
Post-Segregational Killing, Altruistic Cell Death, and Other Toxin/Antitoxin Fallacies (2018)

The toxin/antitoxin (TA) field, born of controversy, is plagued by several prevailing misperceptions. For example, some TA systems stabilize plasmids and other genomic regions; however, the evidence of post-segregational killing by toxins of TA systems is weak. In addition, there are few credible reports of cell death via TA systems like MazF/MazE and via phage exclusion systems. Although many aspects of the biological roles of TA systems remain enigmatic, there are now some clear, confirmed TA functions: (i) phage inhibition, (ii) plasmid maintenance, (iii) stress response (including regulation of loci distinct from the TA pair itself), (iv) biofilm formation, and (v) persistence. Therefore, this opinion piece aims to challenge the oft-repeated dogma related to TA systems with the goal of emphasizing their primary biological role: constraining metabolism in a reversible manner. Hence, their roles in their five confirmed functions all stem from their ability to rapidly and reversibly reduce metabolic activity.
A Weighted Scheduling Mechanism to Reduce Multicast Packet Loss in IPTV Service over EPON (2009)

This letter proposes a weighted scheduling mechanism for Internet protocol television (IPTV) to improve the loss performance of multicast transmission over an Ethernet passive optical network (EPON). We propose a new weight policy from the number of multicast receivers to proportionally allocate the downstream bandwidth of IPTV traffic. The proposed mechanism is used in an optical line terminal to decrease lost packets of favorite IPTV services because the lost multicast packets are proportional to the number of receivers. The total proportion of lost multicast packets is reduced by up to 73% in an EPON.