Miracle-dz/UniFAR-FTUs huggingface dataset:
[11C]metomidate positron emission tomography of adrenocortical tumors in correlation with histopathological findings.

CONTEXT Adrenal incidentalomas are common findings necessitating extensive laboratory work-up and repetitive radiological examinations. Positron emission tomography (PET) using (11)C-labeled metomidate (MTO) has previously been described as a tool for specific adrenocortical imaging. OBJECTIVE We evaluated 212 MTO-PET examinations in 173 patients to identify its role in the management of adrenal tumors. DESIGN Seventy-five histopathological examinations from 73 patients were retrospectively analyzed. SETTING All examinations were performed at a referral center. PATIENTS Patients who were operated or biopsied due to adrenal tumors had histopathological diagnoses of adrenocortical adenoma (n = 26), adrenocortical cancer (ACC; n = 13), adrenocortical hyperplasia (n = 8), pheochromocytoma (n = 6), metastasis (n = 3), and tumors of nonadrenal origin (n = 19). MAIN OUTCOME MEASURES The main outcome measures were statistical analyses and findings while scrutinizing images. The hypothesis that MTO-PET is of value in the management of adrenal tumors, especially incidentaloma, was stated before data collection. RESULTS Sensitivity was 0.89 and specificity was 0.96 for MTO-PET in proving adrenocortical origin of the lesions. Pheochromocytomas, metastases to the adrenal gland, and nonadrenal masses were all MTO negative. PET measurements using standardized uptake values (SUV) in pathological adrenocortical tissue could differentiate lesions larger than 1-1.5 cm from normal adrenocortical tissue. SUV was higher in aldosterone-hypersecreting adenomas, and the SUV ratio between the tumor and the contralateral gland was significantly higher in all hormonally hypersecreting adenomas as well as in ACC. CONCLUSION MTO-PET is a specific and sensitive method for diagnosing adrenocortical tumors. MTO-PET is useful in the imaging work-up of adrenal incidentalomas and may be beneficial for the examination of patients with primary aldosteronism or ACC.
ESpritz: accurate and fast prediction of protein disorder

MOTIVATION Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications. RESULTS In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a S(w) measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. CONCLUSIONS ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. AVAILABILITY Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio. unipd.it/espritz/.
The Contribution of L-Type Cav1.3 Channels to Retinal Light Responses

L-type voltage-gated calcium channels (LTCCs) regulate tonic neurotransmitter release from sensory neurons including retinal photoreceptors. There are three types of LTCCs (Cav1.2, Cav1.3, and Cav1.4) expressed in the retina. While Cav1.2 is expressed in all retinal cells including the Müller glia and neurons, Cav1.3 and Cav1.4 are expressed in the retinal neurons with Cav1.4 exclusively expressed in the photoreceptor synaptic terminals. Mutations in the gene encoding Cav1.4 cause incomplete X-linked congenital stationary night blindness in humans. Even though Cav1.3 is present in the photoreceptor inner segments and the synaptic terminals in various vertebrate species, its role in vision is unclear, since genetic alterations in Cav1.3 are not associated with severe vision impairment in humans or in Cav1.3-null (Cav1.3−/−) mice. However, a failure to regulate Cav1.3 was found in a mouse model of Usher syndrome, the most common cause of combined deafness and blindness in humans, indicating that Cav1.3 may contribute to retinal function. In this report, we combined physiological and morphological data to demonstrate the role of Cav1.3 in retinal physiology and function that has been undervalued thus far. Through ex vivo and in vivo electroretinogram (ERG) recordings and immunohistochemical staining, we found that Cav1.3 plays a role in retinal light responses and synaptic plasticity. Pharmacological inhibition of Cav1.3 decreased ex vivo ERG a- and b-wave amplitudes. In Cav1.3−/− mice, their dark-adapted ERG a-, b-wave, and oscillatory potential amplitudes were significantly dampened, and implicit times were delayed compared to the wild type (WT). Furthermore, the density of ribbon synapses was reduced in the outer plexiform layer of Cav1.3−/− mice retinas. Hence, Cav1.3 plays a more prominent role in retinal physiology and function than previously reported.
Ascending auditory afferents to the nuclei of the lateral leminscus

Afferents from the hindbrain auditory system to the nuclei of the lateral lemniscus were analyzed by the use of orthograde and retrograde axontracing techniques. Three divisions of the nuclei of the lateral lemniscus, a dorsal, an intermediate, and a ventral division are discussed. The dorsal nucleus of the lateral lemniscus is a recipient of afferents from cells located mainly in the superior olivary complex and the contralateral dorsal nucleus of the lateral lemniscus. It receives direct afferents from only a few cells in the cochlear nuclei. In sharp contrast, the ventral nucleus of the lateral lemniscus is the recipient of afferents from many cells in the contralateral ventral cochlear nucleus and from only a few cells in the superior olivary complex. Further, it receives no afferents from cells in the contralateral nuclei of the lateral lemniscus. The intermediate nucleus of the lateral lemniscus receives afferents from some cells in the cochlear nucleus and the superior olivary complex. It is unique among the three nuclei of the lateral lemniscus in that it receives a substantial projection from the medial nucleus of the trapezoid body.
Envelope Amplifier Based on Switching Capacitors for High-Efficiency RF Amplifiers

Modern transmitters usually have to amplify and transmit signals with simultaneous envelope and phase modulation. Due to this property of the transmitted signal, linear power amplifiers (class A, B, or AB) are usually used as a solution for the power amplifier stage. These amplifiers have high linearity, but suffer from low efficiency when the transmitted signal has high peak-to-average power ratio. The Kahn envelope elimination and restoration technique is used to enhance the efficiency of RF transmitters, by combining highly efficient, nonlinear RF amplifier (class E) with a highly efficient envelope amplifier in order to obtain a linear and highly efficient RF amplifier. This paper presents a solution for the envelope amplifier based on a multilevel converter in series with a linear regulator. The multilevel converter is implemented by employing voltage dividers based on switching capacitors. The implemented envelope amplifier can reproduce any signal with a maximum spectral component of 2 MHz and give instantaneous maximum power of 50 W. The efficiency measurements show that when the signals with low average value are transmitted, the implemented prototypes have up to 20% higher efficiency than linear regulators used as a conventional solution.
The Ongoing Search for the Neuronal Correlate of Consciousness

A few decades ago the search for the neuronal correlates of consciousness was considered both technically intractable and philosophically questionable. Searching for a material substrate of phenomena accessible only from the first-person perspective appeared to be epistemically problematic. But the development of non-invasive imaging technologies and the availability of intracranial recordings from patients alleviated the imminent technical problems. Progress in the analysis of the connectome of the brain, and the introduction of multisite recordings from the cerebral cortex of animals led to a revision of concepts in the field of cognitive neuroscience, emphasizing principles of distributed processing in recurrent networks with non-linear dynamics, self-organization, and coding in high-dimensional-state space. These advances, together with the growing evidence for epigenetic shaping of brain functions by socio-cultural influences, pave the way for novel theories that attempt to bridge the gap between neuronal processes and subjective states.
Broken SU(4) symmetry in a Kondo-correlated carbon nanotube

Understanding the interplay between many-body phenomena and nonequilibrium in systems with entangled spin and orbital degrees of freedom is a central objective in nanoelectronics. We demonstrate that the combination of Coulomb interaction, spin-orbit coupling, and valley mixing results in a particular selection of the inelastic virtual processes contributing to the Kondo resonance in carbon nanotubes at low temperatures. This effect is dictated by conjugation properties of the underlying carbon nanotube spectrum at zero and finite magnetic field. Our measurements on a clean carbon nanotube are complemented by calculations based on a field-theoretical Keldysh approach to the nonequilibrium Kondo problem which well reproduces the rich experimental observations in Kondo transport.
Visualizing, Summarizing, and Comparing Odds Ratio Structures

Abstract. The odds ratio is one of the main measures of association in 2 × 2 tables. For larger tables, summary measures of association have been proposed as well as modeling strategies, where the odds ratios can be deduced from the parameters of a model. We propose a computationally simple scaling methodology, which gives a summary measure of association and a visualization of the odds ratio structure. Different variants of the methodology are discussed and compared, both theoretically and empirically. The methodology is also generalized to multiple tables, where not only the structure of each table is important, but also comparisons among tables.
Periodicity Analysis using An Harmonic Matching method and Bandwise Processing

In this paper, two methods for fundamental frequency estimation are compared in order to study the advantages of using a bandwise processing for periodicity analysis. The first one is a harmonic matching algorithm that tries to match the peaks of the magnitude spectrum to a harmonic series. The second one splits the signal in separate frequency bands and computes an estimate for each band. Finally, the result is combined to obtain a global estimate.
The Pupillary Response in Traumatic Brain Injury: A Guide for Trauma Nurses

Traumatic brain injuries (TBIs) affect more than 1.4 million Americans annually. Trauma nurses caring for these patients routinely perform serial neurologic assessments, including pupillary examinations. While trauma nurses are likely familiar with basic components of the pupillary examination, some confusion about more specific aspects of the examination and the physiologic basis of the pupillary response may still remain, particularly as it pertains to patients with TBI. Therefore, the purpose of this article is to identify the key components of a pupillary examination and its associated physiologic response. A case study is provided to illustrate the application of this information among patients with TBI.
The use of brush cytology and directed biopsies for the detection of nasopharyngeal carcinoma and precursor lesions

It has been proposed that nasopharyngeal carcinoma (NPC) has an early noninvasive stage, designated nasopharyngeal intraepithelial neoplasia (NPIN). Hence, the detection and treatment of NPIN will prevent NPC from developing, and this would be similar to the strategies used for cervical cancer prevention. We wanted to ascertain the feasibility of using a brush sampler to collect cells for the cytologic diagnosis of NPIN and NPC. If successful, the technique could be used as a screening test in endemic areas.
Toll‐like receptor signaling inhibits structural development of the distal fetal mouse lung

We tested the hypothesis that innate immune signaling in utero could disrupt the structural development of the fetal lung, contributing to the pathogenesis of bronchopulmonary dysplasia. Injection of Escherichia coli lipopolysaccharide (LPS) into the amniotic fluid of E15 BALB/cJ mice increased the luminal volume density of fetal mouse lungs at embryonic day (E) 17 and E18. LPS also increased luminal volume and decreased distal lung branching in fetal mouse lung explants. This effect required NF‐κB activation and functional Toll‐Like Receptor 4. Airway branching may require fibronectin‐dependent epithelial–mesenchymal interactions, representing a potential target for innate immune signaling. Anti‐fibronectin antibodies and LPS both blocked distal lung branching. By immunofluorescence, fibronectin localized to the clefts between newly formed airways but was restricted to peripheral mesenchymal cells in LPS‐exposed explants. These data suggest that LPS may alter the expression pattern of mesenchymal fibronectin, potentially disrupting epithelial–mesenchymal interactions and inhibiting distal airway branching and alveolarization. This mechanism may link innate immune signaling with defects in structural development of the fetal lung. Developmental Dynamics 233:553–561, 2005. © 2005 Wiley‐Liss, Inc.
ORMDL orosomucoid-like proteins are degraded by free-cholesterol-loading–induced autophagy

Significance Accumulation of toxic lipids in macrophages or human plaques leads to endoplasmic reticulum (ER) stress and induction of autophagy. However, the mechanism by which ER stress and autophagy help in fine tuning cellular lipid homeostasis to counter free-cholesterol toxicity is not clear. Our studies demonstrate that cholesterol induces the translocation of ORMDL orosomucoid-like proteins out of the ER and targets them to autophagosomes, thereby relieving their negative regulation on cellular de novo sphingolipid synthesis. In addition, ORMDL3 has been recently implicated in childhood asthma and in eosinophil trafficking and activation. Thus, our finding of increased turnover of ORMDL proteins by free cholesterol is relevant not only in context to atherosclerotic disease progression but may also shed new insights on lipid homeostasis in other human diseases. Eukaryotic cells have evolved robust mechanisms to counter excess cholesterol including redistribution of lipids into different compartments and compensatory up-regulation of phospholipid biosynthesis. We demonstrate here that excess cellular cholesterol increased the activity of the endoplasmic reticulum (ER) enzyme serine palmitoyl-CoA transferase (SPT), the rate-limiting enzyme in sphingomyelin synthesis. This increased SPT activity was not due to altered levels of SPTLC1 or SPTLC2, the major subunits of SPT. Instead, cholesterol loading decreased the levels of ORMDL1, a negative regulator of SPT activity, due to its increased turnover. Several lines of evidence demonstrated that free-cholesterol–induced autophagy, which led to increased turnover of ORMDL1. Cholesterol loading induced ORMDL1 redistribution from the ER to cytoplasmic p62 positive autophagosomes. Coimmunoprecipitation analysis of cholesterol-loaded cells showed increased association between ORMDL1 and p62. The lysosomal inhibitor chloroquine or siRNA knockdown of Atg7 inhibited ORMDL1 degradation by cholesterol, whereas proteasome inhibitors showed no effect. ORMDL1 degradation was specific to free-cholesterol loading as autophagy induced by serum starvation or general ER stress did not lead to ORMDL1 degradation. ORMDL proteins are thus previously unidentified responders to excess cholesterol, exiting the ER to activate SPT and increase sphingomyelin biosynthesis, which may buffer excess cellular cholesterol.
Impact of siRNA targeting of β-catenin on differentiation of rat neural stem cells and gene expression of Ngn1 and BMP4 following in vitro hypoxic-ischemic brain damage

The aim of the present study was to investigate the possible damage-repair mechanisms of neural stem cells (NSCs) following hypoxic-ischemic brain damage (HIBD). NSCs obtained from Sprague Dawley rats were treated with tissue homogenate from normal or HIBD tissue, and β-catenin expression was silenced using siRNA. The differentiation of NSCs was observed by immunofluorescence, and semiquantitative reverse transcription-polymerase chain reaction and western blot analysis were applied to detect the mRNA and protein expression levels of Ngn1 and BMP4 in the NSCs. Compared with control NSCs, culture with brain tissue homogenate significantly increased the differentiation of NSCs into neurons and oligodendrocytes (P<0.05), whereas differentiation into astrocytes was significantly reduced (P<0.05). Compared with negative control-transfected cells, knockdown of β-catenin expression significantly decreased the differentiation of NSCs into neurons and oligodendrocytes (P<0.01), whereas the percentage of NSCs differentiated into astrocytes was significantly increased (P<0.01). Compared with control NSCs, the mRNA and protein expression levels of Ngn1 were significantly increased (P<0.01) and BMP4 levels were significantly reduced (P<0.01) by exposure of the cells to brain tissue homogenate. Compared with the negative control plasmid-transfected NSCs, the levels of Ngn1 mRNA and protein were significantly reduced by β-catenin siRNA (P<0.01), whereas BMP4 levels were significantly increased (P<0.01). In summary, the damaged brain tissues in HIBD may promote NSCs to differentiate into neurons for self-repair processes. β-Catenin, BMP4 and Ngn1 may be important for the coordination of NSC proliferation and differentiation following HIBD.
Bandwidth Potential, Electromagnetic and Duplex Isolation of Tunable Capacitive Coupling Element Antennas for 4G Smartphones

Current antenna design includes radiating elements whose performance is difficult to analyze with standard performance metrics such as scattering parameters. In this paper we present simulation results analyzing different Capacitive Coupling Elements (CCEs) tunable antenna topologies for 4G smartphones. Scattering parameters, tuning range and novel performance metrics such as both electromagnetic and duplex isolation are presented. It is found that the arrangement of radiators on the groundplane has a significant effect in determining the mutual coupling level, while configurations exhibiting a high bandwidth potential also lead to low isolation. Electromagnetic isolation also depends on the topology, while the duplex isolation is similar for each configuration as they represent comparable volumes on the groundplane.
Direct evidence for a two‐state protein unfolding transition from hydrogen‐deuterium exchange, mass spectrometry, and NMR

We use mass spectrometry in conjunction with hydrogen‐deuterium exchange and NMR to characterize the conformational dynamics of the 62‐residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (>105/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at ∼0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR‐derived estimates of the proton exchange rates.
GROUP DIFFUSION LMS Jie Chen ?

Considering groups of variables, rather than variables individually, can be beneficial for estimation accuracy if structural relationships between variables exist (e.g., spatial, hierarchical or related to the physics of the problem). Group-sparsity inducing estimators are typical examples that benefit from such type of prior knowledge. Building on this principle, we show that the diffusion LMS algorithm for distributed inference over networks can be extended to deal with structured criteria built upon groups of variables, leading to a flexible framework that can encode various structures in the parameters to estimate. We also propose an unsupervised online strategy to differentially promote or inhibit collaborations between nodes depending on the group of variables at hand.
Combined Venom Gland Transcriptomic and Venom Peptidomic Analysis of the Predatory Ant Odontomachus monticola

Ants (hymenoptera: Formicidae) have adapted to many different environments and have become some of the most prolific and successful insects. To date, 13,258 ant species have been reported. They have been classified into 333 genera and 17 subfamilies. Except for a few Formicinae, Dolichoderinae, and members of other subfamilies, most ant species have a sting with venom. The venoms are composed of formic acid, alkaloids, hydrocarbons, amines, peptides, and proteins. Unlike the venoms of other animals such as snakes and spiders, ant venoms have seldom been analyzed comprehensively, and their compositions are not yet completely known. In this study, we used both transcriptomic and peptidomic analyses to study the composition of the venom produced by the predatory ant species Odontomachus monticola. The transcriptome analysis yielded 49,639 contigs, of which 92 encoded toxin-like peptides and proteins with 18,106,338 mapped reads. We identified six pilosulin-like peptides by transcriptomic analysis in the venom gland. Further, we found intact pilosulin-like peptide 1 and truncated pilosulin-like peptides 2 and 3 by peptidomic analysis in the venom. Our findings related to ant venom peptides and proteins may lead the way towards development and application of novel pharmaceutical and biopesticidal resources.