gebhart/patrepeval huggingface dataset:
QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results (2021)

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at: https://github.com/RagMeh11/QU-BraTS.
In-fiber acousto-optic frequency shifter (1991)

An all-fiber frequency shifter has been developed, based on acousto-optically induced intermodal coupling in a dual-mode fiber at 1.3 μm. We have incorporated several design variations on earlier device configurations 1-3 which provide a more robust modulator with the potential for greater spurious signal suppression.
Promotion of Joint Degeneration and Chondrocyte Metabolic Dysfunction by Excessive Growth Hormone in Mice (2023)

This study showed that an excessive amount of GH promotes joint degeneration in mice, which was associated with chondrocyte metabolic dysfunction and hypertrophic changes, whereas antagonizing GH action through a GHa protects mice from OA development.
Supplementary Figure 2 from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers (2023)

&lt;p&gt;Supplementary Figure 2 - PDF file 17K, SKIL induces Matrigel invasion&lt;/p&gt;
At the end of the lecture (2007)

A very important and often neglected aspect of lectures is the way in which the lecture ends. Again, if we consider the television show analogy, the ending of most episodes is exciting, concluding, happy, and sometimes, involves a cliffhanger to motivate the viewers to watch further episodes. A lecture, in a very similar way, needs to end on a positive note while providing ample motivation for the audience to get excited about what they have just experienced. As a result, great care must be taken in the last few minutes of a lecture to end on a high note. For example, rushing to finish an example quickly due to the lack of time can have very negative consequences, as is the case when a topic causes confusion in the last moments of the lecture with no time to clarify the situation or to answer questions.
Spectrum sharing for next generation wireless communication networks (2008)

Future wireless services are expected to provide data-rates in the order of 1 Gbps in local area and 100 Mbps in wide area. A very wide bandwidth is required to support such high rates, in the order of 100 MHz: this wideband will not be available for each operator, thus a shared access to the spectrum among operators is needed. An holistic approach to spectrum sharing is adopted in this paper: not a single layer or component is optimized, but the system as a whole. Advanced physical layer (PHY) and radio resource management (RRM) solutions, utilizing some cognitive radio concepts, are discussed.
French folktales from the collection of Henri Pourrat (1989)

Selected from Henri Pourrat's classic Le tresor des contes, one of the finest folktale collections in the world, these one-hundred-odd legends, fairy tales, devotional pieces, jokes, and animal stories from the rural provinces of France comprise a magical volume. Fairies, changelings, giants, demons, bumpkins, knaves, bewitched and bewitching princesses, bandits, and others enact stories of perilous tests of love, contests with the devil, the beneficence of saints, and more. Royall Tyler's translation deftly captures the vigor and resonance of the originals, and his cogent introduction illuminates for the reader the earthy, chilling, mischievous, and mystical realm these tales evoke. From the Trade Paperback edition.
Frontline Science: A flexible kink in the transmembrane domain impairs β2 integrin extension and cell arrest from rolling (2019)

β2 integrins are the main adhesion molecules in neutrophils and other leukocytes and are rapidly activated by inside-out signaling, which results in conformational changes that are transmitted through the transmembrane domain (TMD). Here, we investigated the biologic effect of introducing a proline mutation in the β2 integrin TMD to create a flexible kink that uncouples the topology of the inner half of the TMD from the outer half and impairs integrin activation. The β2 integrin alpha chains, αL, αM, αX, and αD, all contain an inserted (I) domain with homology to von Willebrand factor A domain. β2 activation was monitored in a homogenous binding assay of 2 reporter monoclonal antibodies: KIM127 reporting extension (E<sup>+</sup> ) and mAb24 reporting the high-affinity (H<sup>+</sup> ) conformation of the β2 I-like domain. The proline mutation partially diminished chemokine-induced extension, but not the high-affinity conformation. The proline mutation in the TMD of β2 completely inhibited arrest of rolling HL-60 cells in response to the chemokine IL-8. TMD mutant HL-60 cells rolling on P-selectin and ICAM-1 were unable to reduce their rolling velocity in response to IL-8. Quantitative dynamic footprinting live-cell imaging showed that blocking TMD topology transmission impaired the chemokine-induced activation of β2, limiting the appearance of extended high-affinity (E<sup>+</sup> H<sup>+</sup> ) β2. This also resulted in a defect in early spreading (3 min after arrest), which could be overcome by forced integrin activation using Mn<sup>2+</sup> . We conclude that the TMD proline mutation severely impairs β2 integrin extension, cell arrest, and early spreading.
Early Pregnancy Sex Steroids and Maternal Breast Cancer: A Nested Case-Control Study (2015)

Pregnancy, parity, and circulating steroid hormone levels are associated with risk of breast cancer, but little is known about hormone concentrations during pregnancy and subsequent breast cancer risk. We evaluated early pregnancy (<140 days gestation) serum estradiol, estrone, progesterone, and testosterone and breast cancer risk in a nested case-control study in the Finnish Maternity Cohort. The cohort includes 98% of pregnancies registered in Finland since 1983. Individuals with samples collected in the first pregnancy leading to a live birth were eligible. Breast cancer cases (n = 1,199) were identified through linkage with the Finnish Cancer Registry; 2,281 matched controls were selected using incidence density sampling. ORs were calculated using conditional logistic regression. Hormone concentrations were not associated with breast cancer overall. Estradiol was positively associated with risk of breast cancer diagnosed age <40 [4th vs. 1st quartile OR 1.60 (1.07-2.39); Ptrend = 0.01], and inversely associated with breast cancer diagnosed at age ≥40 [4th vs. 1st quartile OR 0.71 (0.51-1.00); Ptrend = 0.02]. Elevated concentrations of the steroid hormones were associated with increased risk of estrogen receptor (ER)- and progesterone receptor (PR)-negative tumors in women age <40 at diagnosis. We observed no association between steroid hormones and ER(+)/PR(+) disease. These data suggest a positive association between high concentrations of early pregnancy steroid hormones and risk of ER(-)/PR(-) breast cancer in women diagnosed age <40, and an inverse association for overall breast cancer diagnosed age ≥40. Further research on pregnancy hormones and risk of steroid receptor-negative cancers is needed to further characterize this association.
Search for the doubly charmed baryon $\it{\Xi}_{cc}^{+}$ in the $\it{\Xi}_{c}^{+} \pi^{-} \pi^{+}$ final state (2021)

A search for the doubly charmed baryon $\it{\Xi}_{cc}^{+}$ is performed in the $\it{\Xi}_{c}^{+} \pi^{-} \pi^{+}$ invariant-mass spectrum, where the $\it{\Xi}_{c}^{+}$ baryon is reconstructed in the $p K^{-} \pi^{+}$ final state. The study uses proton-proton collision data collected with the LHCb detector at a centre-of-mass energy of 13$\mathrm{\,Te\kern -0.1em V}$, corresponding to a total integrated luminosity of 5.4$\,\mathrm{fb}^{-1}$. No significant signal is observed in the invariant-mass range of 3.4$-$3.8$\mathrm{\,Ge\kern -0.1em V}/c^2$. Upper limits are set on the ratio of branching fractions multiplied by the production cross-section with respect to the $\it{\Xi}_{cc}^{++} \rightarrow (\it{\Xi}_{c}^{+} \rightarrow p K^{-} \pi^{+}) \pi^{+}$ decay for different $\it{\Xi}_{cc}^{+}$ mass and lifetime hypotheses in the rapidity range from 2.0 to 4.5 and the transverse momentum range from 2.5 to 25$\mathrm{\,Ge\kern -0.1em V}/c$. The results from this search are combined with a previously published search for the $\it{\Xi}_{cc}^{+} \rightarrow \it{\Lambda}_{c}^{+} K^{-} \pi^{+}$ decay mode, yielding a maximum local significance of 4.0 standard deviations around the mass of 3620$\mathrm{\,Me\kern -0.1em V}/c^2$, including systematic uncertainties. Taking into account the look-elsewhere effect in the 3.5$-$3.7$\mathrm{\,Ge\kern -0.1em V}/c^2$ mass window, the combined global significance is 2.9 standard deviations including systematic uncertainties.
Endoscopic ultrasonography-guided fine-needle aspiration in the management of mediastinal diseases: local experience of a novel investigation. (2010)

Trans-oesophageal endoscopic ultrasonography-guided fine-needle aspiration is a minimally invasive, effective, and safe method of diagnosing malignant mediastinal disease. It may reduce the need for other invasive investigations.
Use of a persistent photoconductive array in the learning of an optoelectronic neural processor (1991)

Persistent photoconductors of npnp doping-modulated amorphous silicon multilayers are investigated for the implementation of variable analog and nonvolatile synaptic weights of an optoelectronic neural processor. The time dependence of the persistent photoconductance of the amorphous silicon multilayers is characterized in experiments. The learning performance of an optical pattern classifier with the persistent photoconductive array is analyzed by computer simulations.
Entropy of Entropy: Measurement of Dynamical Complexity for Biological Systems (2017)

Healthy systems exhibit complex dynamics on the changing of information embedded in physiologic signals on multiple time scales that can be quantified by employing multiscale entropy (MSE) analysis. Here, we propose a measure of complexity, called entropy of entropy (EoE) analysis. The analysis combines the features of MSE and an alternate measure of information, called superinformation, useful for DNA sequences. In this work, we apply the hybrid analysis to the cardiac interbeat interval time series. We find that the EoE value is significantly higher for the healthy than the pathologic groups. Particularly, short time series of 70 heart beats is sufficient for EoE analysis with an accuracy of 81% and longer series of 500 beats results in an accuracy of 90%. In addition, the EoE versus Shannon entropy plot of heart rate time series exhibits an inverted U relationship with the maximal EoE value appearing in the middle of extreme order and disorder.
fourMs, University of Oslo --- Lab Report (2010)

The paper reports on the development and activities in the recently established fourMs lab (Music, Mind, Motion, Machines) at the University of Oslo, Norway. As a meeting place for researchers in music and informatics, the fourMs lab is centred around studies of basic issues in music cognition, machine learning and robotics.
Antigen Receptor Engagement Turns off the V(D)J Recombination Machinery in Human Tonsil B Cells (1998)

The germinal center (GC) is an anatomic compartment found in peripheral lymphoid organs, wherein B cells undergo clonal expansion, somatic mutation, switch recombination, and reactivate immunoglobulin gene V(D)J recombination. As a result of somatic mutation, some GC B cells develop higher affinity antibodies, whereas others suffer mutations that decrease affinity, and still others may become self-reactive. It has been proposed that secondary V(D)J rearrangements in GCs might rescue B cells whose receptors are damaged by somatic mutations. Here we present evidence that mature human tonsil B cells coexpress conventional light chains and recombination associated genes, and that they extinguish recombination activating gene and terminal deoxynucleotidyl transferase expression when their receptors are cross-linked. Thus, the response of the recombinase to receptor engagement in peripheral B cells is the opposite of the response in developing B cells to the same stimulus. These observations suggest that receptor revision is a mechanism for receptor diversification that is turned off when antigen receptors are cross-linked by the cognate antigen.
Scintillation Properties of Dy-doped 50NaPO3–50Al(PO3)3 Glasses (2021)

5, 1.0, 5.0, and 10.0 mol% Dy-doped 50NaPO 3 -50Al(PO 3 ) 3 glasses were synthesized by the melt-quenching method. All the samples had a high transmittance of up to 90% at visible wavelengths, and some intense emission lines were observed in their photoluminescence and scintillation spectra. When the glasses were irradiated with X-rays with various doses, a linear relationship between the irradiation dose and the thermally stimulated luminescence intensity was confirmed from 10 to 10000 mGy.
Anesthesia for Fetal Intervention (2000)

The anesthetic management for the fetal operation on placental support procedure has been previously described (1–3). However, the advantages of combining general with regional anesthesia/analgesia for this procedure has not been described. A 21-yr-old, gravida 2, para 1 parturient was referred to our hospital for cesarean delivery and the operation on placental support procedure. Early in her pregnancy, she had been diagnosed as having polyhydramnios. Subsequent investigation by using ultrasound and magnetic resonance imaging revealed that the fetus had an extremely large cervical teratoma–extending from the base of the tongue to the sternal notch–which completely occluded the trachea. An epidural catheter was sited at the L2-3 interspace. After the induction of anesthesia, profound uterine relaxation was maintained with sevoflurane (end tidal 2.8%–2.9%) in 100% oxygen during cesarean delivery while a surgical airway was established in the fetus. With the baby delivered but with placental circulation still intact, direct laryngoscopy, followed by rigid bronchoscopy, revealed that intubation was not possible. Therefore, a surgical airway was established via a tracheostomy. The umbilical cord was then clamped, and 5 units of oxytocin was given IV, followed by an oxytocin infusion. Sevoflurane was discontinued immediately to facilitate uterine contraction. Analgesia was provided with 10 mL of bupivacine 0.25% and 100 μg of fentanyl via the epidural catheter in divided doses over the following 10 minutes, and midazolam 2 mg and fentanyl 100 μg were administered IV to supplement anesthesia. Surgery was completed in 45 minutes. The patient was comfortable on awakening. Total blood loss was 1000 mL. Postoperative analgesia was provided with a continuous infusion of 0.125% bupivacine with fentanyl 2 μg/mL. Three milligrams of preservative-free morphine was administered before the removal of the epidural catheter the following morning. Apart from providing intraoperative and postoperative analgesia, the presence of an epidural catheter allows complete discontinuation of the volatile agent after cord clamping. This should promote immediate and sustained uterine contraction and, therefore, reduce the likelihood of uterine atony and subsequent massive obstetric hemorrhage. Miriam J. P. Harnett MB, FFARCSI Ronald Hurley MD
High-fat diet-induced atherosclerosis promotes neurodegeneration in the triple transgenic (3 × Tg) mouse model of Alzheimer’s disease associated with chronic platelet activation (2021)

These findings suggest that a major contribution of atherosclerosis to AD pathology is via its effects on blood coagulation and the formation of platelet-mediated Aβ aggregates that compromise cerebral blood flow and therefore neuronal function. This leads to cognitive decline.
Abstract 4417: Targeting Ras with small molecules that activate SOS-mediated nucleotide exchange (2014)

Abstract Aberrant activation of Ras, by mutation or constitutively active upstream kinases, occurs in nearly 30% of all human cancers, rendering Ras one of the most validated targets in cancer drug discovery. Historically, the direct inhibition of Ras with small molecules has proven extremely difficult. Here we report the discovery of compounds that bind to a unique pocket on the Ras:SOS:Ras complex, which increase the rate of SOScat-catalyzed nucleotide exchange in vitro and modulate Ras signaling pathways in cells. X-ray crystallography reveals that the molecules bind in a hydrophobic pocket in the CDC25 domain of SOS, adjacent to the Switch II region of Ras. Structure-based mutational analyses confirmed the functional relevance of this binding site and demonstrated that it is essential for compound activity. Consistent with their increased exchange activity in vitro, these molecules increase Ras-GTP levels in cells. However, the compounds inhibit ERK and AKT phosphorylation; the ERK inhibition at high concentrations is accompanied by an increase of p-ERK levels at lower compound concentrations. These molecules represent a unique tool to study the acute activation of Ras and highlight a novel pocket on SOS that may be exploited to modulate Ras signaling. Citation Format: Olivia W. Rossanese, Michael C. Burns, Qi Sun, R. Nathan Daniels, DeMarco V. Camper, J. Phillip Kennedy, Jason Phan, Edward T. Olejniczak, Taekyu Lee, Alex G. Waterson, Stephen W. Fesik. Targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4417. doi:10.1158/1538-7445.AM2014-4417
The Effective Thermal Conductivity of a Bed of 1.2-mm-diam Lithium Zirconate Spheres in Helium (1998)

The effective thermal conductivity of a bed of lithium zirconate spheres in helium has been measured over the ranges 0 < P < 200 kPa and 600 < T < 1500 K. The data are fitted to the equation k = ap + bpT3. At 100 kPa, the thermal conductivity is given by k(T) = 0.69 + 2.2 × 10-10 T3 W/m·K-1. A table of values for ap and bp is provided for other pressure settings. Values of the near-wall effective thermal conductivity are estimated from the data.
Supplementary methods and figure legends from Resistance to Anti-VEGF Therapy Mediated by Autocrine IL6/STAT3 Signaling and Overcome by IL6 Blockade (2023)

&lt;p&gt;Supplementary methods and figure legends&lt;/p&gt;
Supplemental Figure Legends from Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer (2023)

&lt;p&gt;Supplemental Figure Legends&lt;/p&gt;
VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis (2022)

VISTA (V domain immunoglobulin suppressor of T cell activation, also called PD-1H [programmed death-1 homolog]), a novel immune regulator expressed on myeloid and T lymphocyte lineages, is upregulated in mouse and human idiopathic pulmonary fibrosis (IPF). However, the significance of VISTA and its therapeutic potential in regulating IPF has yet to be defined. To determine the role of VISTA and its therapeutic potential in IPF, the expression profile of VISTA was evaluated from human single-cell RNA sequencing data (IPF Cell Atlas). Inflammatory response and lung fibrosis were assessed in bleomycin-induced experimental pulmonary fibrosis models in VISTA-deficient mice compared with wild-type littermates. In addition, these outcomes were evaluated after VISTA agonistic antibody treatment in the wild-type pulmonary fibrosis mice. VISTA expression was increased in lung tissue-infiltrating monocytes of patients with IPF. VISTA was induced in the myeloid population, mainly circulating monocyte-derived macrophages, during bleomycin-induced pulmonary fibrosis. Genetic ablation of VISTA drastically promoted pulmonary fibrosis, and bleomycin-induced fibroblast activation was dependent on the interaction between VISTA-expressing myeloid cells and fibroblasts. Treatment with VISTA agonistic antibody reduced fibrotic phenotypes accompanied by the suppression of lung innate immune and fibrotic mediators. In conclusion, these results suggest that VISTA upregulation in pulmonary fibrosis may be a compensatory mechanism to limit inflammation and fibrosis, and stimulation of VISTA signaling using VISTA agonists effectively limits the fibrotic innate immune landscape and consequent tissue fibrosis. Further studies are warranted to test VISTA as a novel therapeutic target for the IPF treatment.
Review MUC1 and cancer (1999)

The MUC1 membrane mucin was first identified as the molecule recognised by mouse monoclonal antibodies directed to epithelial cells, and the cancers which develop from them. Cloning the gene showed that the extracellular domain is made up of highly conserved repeats of 20 amino acids, the actual number varying between 25 and 100 depending on the allele. Each tandem repeat contains five potential glycosylation sites, and between doublets of threonines and serines lies an immunodominant region which contains the epitopes recognised by most of the mouse monoclonal antibodies. The Oglycans added to the mucin produced by the normal breast are core 2 based and can be complex, while the O-glycans added to the breast cancer mucin are mainly core 1 based. This means that some core protein epitopes in the tandem repeat which are masked in the normal mucin are exposed in the cancer associated mucin. Since novel carbohydrate epitopes are also carried on the breast cancer mucin, the molecule is antigenically distinct from the normal breast mucin. (Changes in glycosylation in other epithelial cancers have been observed but are not so well documented.) Immune responses to MUC1 have been seen in breast and ovarian cancer patients and clinical studies have been initiated to evaluate the use of antibodies to MUC1 and of immunogens based on MUC1 for immunotherapy of these patients. The role of the carbohydrates in the immune response and in other interactions with the effector cells of the immune system is of particular interest and is discussed. fl 1999 Elsevier Science B.V. All rights reserved.