Miracle-dz/UniFAR-FTUs huggingface dataset:
Auditory network connectivity in tinnitus patients: A resting-state fMRI study

Abstract Objective: Resting-state functional magnetic resonance imaging (fMRI) uncovers correlated activity between spatially distinct functionally related brain regions and offers clues about the integrity of functional brain circuits in people with chronic subjective tinnitus. We chose to investigate auditory network connectivity, adopting and extending previously used analyses methods to provide an independent evaluation of replicability. Design: Independent components analysis (ICA) was used to identify coherent patterns arising from spontaneous brain signals within the resting-state data. The auditory network component was extracted and evaluated. Bivariate and partial correlation analyses were performed on pre-defined regions of bilateral auditory cortex to assess functional connectivity. Study sample: Our design carefully matched participant groups for possible confounds, such as hearing status. Twelve patients (seven male, five female; mean age 66 years) all with chronic constant tinnitus and eleven controls (eight male, three female; mean age 68 years) took part. Results: No significant differences were found in auditory network connectivity between groups after correcting for multiple statistical comparisons in the analysis. This contradicts previous findings reporting reduced auditory network connectivity; albeit at a less stringent statistical threshold. Conclusions: Auditory network connectivity does not appear to be reliably altered by the experience of chronic subjective tinnitus.
Metabarcoding analysis of the stomach contents of the Antarctic Toothfish (Dissostichus mawsoni) collected in the Antarctic Ocean

Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms.
Protein Trafficking and Anchoring Complexes Revealed by Proteomic Analysis of Inward Rectifier Potassium Channel (Kir2.x)-associated Proteins*

Inward rectifier potassium (Kir) channels play important roles in the maintenance and control of cell excitability. Both intracellular trafficking and modulation of Kir channel activity are regulated by protein-protein interactions. We adopted a proteomics approach to identify proteins associated with Kir2 channels via the channel C-terminal PDZ binding motif. Detergent-solubilized rat brain and heart extracts were subjected to affinity chromatography using a Kir2.2 C-terminal matrix to purify channel-interacting proteins. Proteins were identified with multidimensional high pressure liquid chromatography coupled with electrospray ionization tandem mass spectrometry, N-terminal microsequencing, and immunoblotting with specific antibodies. We identified eight members of the MAGUK family of proteins (SAP97, PSD-95, Chapsyn-110, SAP102, CASK, Dlg2, Dlg3, and Pals2), two isoforms of Veli (Veli-1 and Veli-3), Mint1, and actin-binding LIM protein (abLIM) as Kir2.2-associated brain proteins. From heart extract purifications, SAP97, CASK, Veli-3, and Mint1 also were found to associate with Kir2 channels. Furthermore, we demonstrate for the first time that components of the dystrophin-associated protein complex, including α1-, β1-, and β2-syntrophin, dystrophin, and dystrobrevin, interact with Kir2 channels, as demonstrated by immunoaffinity purification and affinity chromatography from skeletal and cardiac muscle and brain. Affinity pull-down experiments revealed that Kir2.1, Kir2.2, Kir2.3, and Kir4.1 all bind to scaffolding proteins but with different affinities for the dystrophin-associated protein complex and SAP97, CASK, and Veli. Immunofluorescent localization studies demonstrated that Kir2.2 co-localizes with syntrophin, dystrophin, and dystrobrevin at skeletal muscle neuromuscular junctions. These results suggest that Kir2 channels associate with protein complexes that may be important to target and traffic channels to specific subcellular locations, as well as anchor and stabilize channels in the plasma membrane.
Contradictory influence of context on predominance during binocular rivalry

Background: Binocular rivalry is a complex process characterised by alternations in perceptual suppression and dominance that result when two different images are presented simultaneously to the left and right eyes. It has been reported recently that the addition of contextual cues will promote the predominance of the context consistent rivalry target. In contrast to Levelt' second proposition (1965), this effect has been found to result exclusively from an increase in the dominance phase duration, while the suppression phase duration remains unaffected.
Long-wave theory for a new convective instability with exponential growth normal to the wall

A linear stability theory is presented for the boundary-layer flow produced by an infinite disc rotating at constant angular velocity in otherwise undisturbed fluid. The theory is developed in the limit of long waves and when the effects of viscosity on the waves can be neglected. This is the parameter regime recently identified by the author in a numerical stability investigation where a curious new type of instability was found in which disturbances propagate and grow exponentially in the direction normal to the disc, (i.e. the growth takes place in a region of zero mean shear). The theory describes the mechanisms controlling the instability, the role and location of critical points, and presents a saddle-point analysis describing the large-time evolution of a wave packet in frames of reference moving normal to the disc. The theory also shows that the previously obtained numerical solutions for numerically large wavelengths do indeed lie in the asymptotic long-wave regime, and so the behaviour and mechanisms described here may apply to a number of cross-flow instability problems.
Everything Hertz: methodological issues in short-term frequency-domain HRV

Frequency analysis of the electrocardiographic RR interval is a common method of quantifying autonomic outflow by measuring the beat-to-beat modulation of the heart (heart rate variability; HRV). This review identifies a series of problems with the methods of doing so—the interpretation of low-frequency spectral power, the multiple use of equivalent normalized low frequency (LFnu), high frequency (HFnu) and ratio (LF/HF) terms, and the lack of control over extraneous variables, and reviews research in the calendar year 2012 to determine their prevalence and severity. Results support the mathematical equivalency of ratio units across studies, a reliance on those variables to explain autonomic outflow, and insufficient control of critical experimental variables. Research measurement of HRV has a substantial need for general methodological improvement.
Confocal calcium imaging reveals an ionotropic P2 nucleotide receptor in the paranodal membrane of rat Schwann cells

1 The paranodal Schwann cell region is of major importance for the function of a myelinated axon. In the present study we searched for a possible ionotropic effect of extracellular ATP in this Schwann cell compartment. 2 Whole‐cell patch‐clamp recordings from cultured rat Schwann cells revealed that ATP and 2′–3′‐O‐(4‐benzoylbenzoyl)‐adenosine 5′‐triphosphate (BzATP) induced a non‐specific cation current. The effect of ATP was much enhanced in a Ca2+‐ and Mg2+‐free solution. ADP, UTP and α,β‐methylene adenosine 5′‐triphosphate (α,β‐meATP) had no effect. 3 Confocal Ca2+ imaging of myelinating Schwann cells in isolated rat spinal roots showed a BzATP‐induced rise in the free intracellular Ca2+ concentration in the paranodal Schwann cell cytoplasm whereas α,β‐meATP and 2‐(methylthio)‐adenosine 5′‐triphosphate were without effect. In contrast to the known metabotropic effect of UTP on these Schwann cell regions, the BzATP‐induced Ca2+ signal was not transient, was unaffected by depletion of intracellular Ca2+ stores and dependent on the presence of extracellular Ca2+. 4 These results suggest that an ionotropic ATP receptor with electrophysiological and pharmacological characteristics of the P2X7 subtype of nucleotide receptors is functionally active in myelinating Schwann cells of peripheral nerves. Such a receptor might contribute to Schwann cell reactions in nerve injury or neuropathy.
Robust Local Coordinate Non-negative Matrix Factorization via Maximum Correntropy Criteria

Non-negative matric factorization (NMF) decomposes a given data matrix X into the product of two lower dimensional non-negative matrices U and V. It has been widely applied in pattern recognition and computer vision because of its simplicity and effectiveness. However, existing NMF methods often fail to learn the sparse representation on high-dimensional dataset, especially when some examples are heavily corrupted. In this paper, we propose a robust local coordinate NMF method (RLCNMF) by using the maximum correntropy criteria to overcome such deficiency. Particularly, RLCNMF induces sparse coefficients by imposing the local coordinate constraint over both factors. To solve RLCNMF, we developed a multiplicative update rules and theoretically proved its convergence. Experimental results on popular image datasets verify the effectiveness of RLCNMF comparing with the representative methods.
Endocytosis of the class I major histocompatibility antigen via a phorbol myristate acetate-inducible pathway is a cell-specific phenomenon and requires the cytoplasmic domain [published erratum appears in J Cell Biol 1989 Sep;109(3):1381]

Class I major histocompatibility (MHC) antigens are expressed by virtually all mammalian cells, yet their levels of expression and behavior on the cell surface vary in a cell-specific fashion. A panel of lymphoid (both B and T) and nonlymphoid cell lines was used to study the kinetics of internalization of the H-2Ld class I MHC in different cell types. These studies revealed that endocytosis of H-2Ld occurs by both constitutive and PMA-regulated pathways in lymphoid cells, but only by a PMA-refractory pathway in the nonlymphoid cells tested. Transfectant derivatives of the T lymphoma, EL4, which express wild- type or mutant H-2Ld class I MHC antigens, were used to investigate the requirement for the cytoplasmic domain of the class I MHC antigen for its endocytosis in T lymphocytes. These studies showed that modification or deletion of the cytoplasmic domain of H-2Ld abrogates endocytosis via a PMA-regulated pathway. The role of cytoplasmic domain phosphorylation in PMA-inducible endocytosis was examined. The wild- type H-2Ld antigen is phosphorylated in all cell types examined, and this phosphorylation is up-regulated by PMA treatment. In contrast, cytoplasmic domain mutants of H-2Ld fail to be phosphorylated in vivo, in the presence or absence of PMA. The universality of PMA-inducible hyperphosphorylation of the class I MHC antigen among diverse cell types leads us to conclude that phosphorylation of the cytoplasmic domain, while perhaps necessary, is not sufficient for triggering endocytosis via a PMA-inducible pathway. Furthermore, the results with the cytoplasmic domain mutants of H-2Ld suggest that a structural conformation of the class I MHC cytoplasmic domain is required for endocytosis via this route.
Hierarchical unsupervised learning of facial expression categories

We consider the problem of unsupervised classification of temporal sequences of facial expressions in video. This problem arises in the design of an adaptive visual agent, which must be capable of identifying appropriate classes of visual events without supervision to effectively complete its tasks. We present a multilevel dynamic Bayesian network that learns the high-level dynamics of facial expressions simultaneously, with models of the expressions themselves. We show how the parameters of the model can be learned in a scalable and efficient way. We present preliminary results using real video data and a class of simulated dynamic event models. The results show that our model correctly classifies the input data comparably to a standard event classification approach, while also learning the high-level model parameters.
HIV DNA and antibodies in syringes from injecting drug users: a comparison of detection techniques.

OBJECTIVE Direct HIV testing of individual injecting drug users is not always feasible. As an alternative, we have evaluated the sensitivity and specificity of several techniques for detecting HIV-1-specific products in used syringes. DESIGN Polymerase chain reaction (PCR) and antibody-capture assays were compared using syringes prepared with blood from HIV-1-positive and -negative individuals. METHODS PCR sensitivity was maximized, enabling detection of single copies of HIV-1-specific proviral DNA. The limits of detection from used syringes were determined for PCR by diluting extracts and correlated to CD4+ cell counts. Similarly, limits of detection were determined for enzyme immunoassays (EIA) and Western blot. RESULTS All techniques were highly specific, although with PCR false-positives were detected occasionally. EIA proved more sensitive than Western blot in detecting needles containing HIV-1-infected individuals' blood. Even after prolonged storage of syringes at room temperature, EIA was equal to or better than PCR as an HIV-1 detection technique. The most sensitive method for detecting HIV-1 was the viral-based EIA when the recommended predilution step was omitted. CONCLUSIONS EIA proved preferable to PCR because of their higher sensitivity, absence of false-positives and easier sample preparation and analysis.
Racial Differences in Virologic Failure Associated With Adherence and Quality of Life on Efavirenz-Containing Regimens for Initial HIV Therapy: Results of ACTG A5095

Background:Blacks had higher rates of virologic failure than whites on efavirenz-containing regimens in the AIDS Clinical Trials Group (ACTG) A5095 study; preliminary analyses also suggested an association with adherence. We rigorously examined associations over time among race, virologic failure, 4 self-reported adherence metrics, and quality of life (QOL). Methods:ACTG A5095 was a double-blind placebo-controlled study of treatment-naive HIV-positive patients randomized to zidovudine/lamivudine/abacavir versus zidovudine/lamivudine plus efavirenz versus zidovudine/lamivudine/abacavir plus efavirenz. Virologic failure was defined as confirmed HIV-1 RNA ≥200 copies/mL at ≥16 weeks on study. The zidovudine/lamivudine/abacavir arm was discontinued early because of virologic inferiority. We examined virologic failure differences for efavirenz-containing arms according to missing 0 (adherent) versus at least 1 dose (nonadherent) during the past 4 days, alternative self-reported adherence metrics, and QOL. Analyses used the Fisher exact, log rank tests, and Cox proportional hazards models. Results:The study population included white (n = 299), black (n = 260), and Hispanic (n = 156) patients with ≥1 adherence evaluation. Virologic failure was associated with week 12 nonadherence during the past 4 days for blacks (53% nonadherent failed vs. 25% adherent; P < 0.001) but not for whites (20% nonadherent failed vs. 20% adherent; P = 0.91). After adjustment for baseline covariates and treatment, there was a significant interaction between race and week 12 adherence (P = 0.02). In time-dependent Cox models using self-reports over time to reflect recent adherence, there was a significantly higher failure risk for nonadherent subjects (hazard ratio [HR] = 2.07; P < 0.001). Significant race-adherence interactions were seen in additional models of adherence: missing at least 1 medication dose ever (P = 0.04), past month (P < 0.01), or past weekend (P = 0.05). Lower QOL was significantly associated with virologic failure (P < 0.001); there was no evidence of an interaction between QOL and race (P = 0.39) or adherence (P = 0.51) in predicting virologic failure. Conclusions:There was a greater effect of nonadherence on virologic failure in blacks given efavirenz-containing regimens than in whites. Self-reported adherence and QOL are independent predictors of virologic failure.
Cold urticaria and celiac disease.

■ Abstract Cold urticaria can be associated with blood and thyroid disorders, drugs, or infections. Celiac disease is an autoimmune enteropathy caused by permanent gluten intolerance. It is often associated with other autoimmune diseases, such as chronic idiopathic urticaria. Nevertheless, association with cold urticaria has not yet been described. A boy aged 3 years 8 months presented local urticaria-angioedema when exposed to cold temperatures. An ice cube test was positive and iron defi ciency anemia was demonstrated. He later developed legume intolerance, rhinoconjunctivitis related to pollen sensitization, and asthma. Due to persistence of cold urticaria symptoms and refractory anemia, a test for immunoglobulin A autoantibodies to tissue transglutaminase and an intestinal biopsy were performed. Results of both tests were compatible with celiac disease. A study of human leukocyte antigen indicated a high risk phenotype (HLA, DR6/DR7; DQA 0501, 0201; DQB 0301, 0201). After 7 months of a gluten-free diet, the boy’s anemia resolved and he is free of symptoms when exposed to cold. This is a fi rst description of the possibility of an association between celiac disease and cold urticaria. A poor course of cold urticaria in the absence of evidence of another underlying condition should lead to suspicion of celiac disease.
Sharp-needle intradermal fat grafting (SNIF).

BACKGROUND Reversing the effects of facial aging is best accomplished with a combination of techniques. Minimizing the appearance of fine wrinkles is an essential part of treatment, which can involve resurfacing, intradermal filler injections, or a combination of the two. The quest for the ideal filler material is ongoing, but intradermal fat injections can serve as an inexpensive and safe alternative to classic intradermal fillers. OBJECTIVES The aim of this study was to evaluate the feasibility, validity, and safety of the sharp-needle intradermal fat grafting (SNIF) technique. METHODS The records of 250 consecutive patients treated over a 3-year period with the authors' SNIF technique were reviewed to evaluate the SNIF technique and its results, including complications. RESULTS Results were evaluated by clinical examination and patient photographs. Good improvement was achieved with SNIF, with results lasting more than 1 year, which exceeds the expected duration for resorbable dermal fillers (typically 3 to 6 months). No major complications occurred; the most common minor complications were bruising and swelling. CONCLUSIONS SNIF is a safe and effective alternative to classic resorbable dermal fillers for patients who can accept the minor discomfort involved in extracting fat from the donor site. The harvesting and injection techniques should be performed with precision to achieve favorable results and avoid complications.
Endogenous calcium buffering at photoreceptor synaptic terminals in salamander retina

Calcium operates by several mechanisms to regulate glutamate release at rod and cone synaptic terminals. In addition to serving as the exocytotic trigger, Ca2+ accelerates replenishment of vesicles in cones and triggers Ca2+‐induced Ca2+ release (CICR) in rods. Ca2+ thereby amplifies sustained exocytosis, enabling photoreceptor synapses to encode constant and changing light. A complete picture of the role of Ca2+ in regulating synaptic transmission requires an understanding of the endogenous Ca2+ handling mechanisms at the synapse. We therefore used the “added buffer” approach to measure the endogenous Ca2+ binding ratio (κendo) and extrusion rate constant (γ) in synaptic terminals of photoreceptors in retinal slices from tiger salamander. We found that κendo was similar in both cell types—∼25 and 50 in rods and cones, respectively. Using measurements of the decay time constants of Ca2+ transients, we found that γ was also similar, with values of ∼100 s−1 and 160 s−1 in rods and cones, respectively. The measurements of κendo differ considerably from measurements in retinal bipolar cells, another ribbon‐bearing class of retinal neurons, but are comparable to similar measurements at other conventional synapses. The values of γ are slower than at other synapses, suggesting that Ca2+ ions linger longer in photoreceptor terminals, supporting sustained exocytosis, CICR, and Ca2+‐dependent ribbon replenishment. The mechanisms of endogenous Ca2+ handling in photoreceptors are thus well‐suited for supporting tonic neurotransmission. Similarities between rod and cone Ca2+ handling suggest that neither buffering nor extrusion underlie differences in synaptic transmission kinetics. Synapse 68:518–528, 2014. © 2014 Wiley Periodicals, Inc.
Computational Model of Recurrent Subthalamo-Pallidal Circuit for Generation of Parkinsonian Oscillations

Parkinson's disease is a movement disorder caused by dopamine depletion in the basal ganglia. Abnormally synchronized neuronal oscillations between 8 and 15 Hz in the basal ganglia are implicated in motor symptoms of Parkinson's disease. However, how these abnormal oscillations are generated and maintained in the dopamine-depleted state is unknown. Based on neural recordings in a primate model of Parkinson's disease and other experimental and computational evidence, we hypothesized that the recurrent circuit between the subthalamic nucleus (STN) and the external segment of the globus pallidus (GPe) generates and maintains parkinsonian oscillations, and that the cortical excitatory input to the STN amplifies them. To investigate this hypothesis through computer simulations, we developed a spiking neuron model of the STN-GPe circuit by incorporating electrophysiological properties of neurons and synapses. A systematic parameter search by computer simulation identified regions in the space of the intrinsic excitability of GPe neurons and synaptic strength from the GPe to the STN that reproduce normal and parkinsonian states. In the parkinsonian state, reduced firing of GPe neurons and increased GPe-STN inhibition trigger burst activities of STN neurons with strong post-inhibitory rebound excitation, which is usually subject to short-term depression. STN neuronal bursts are shaped into the 8–15 Hz, synchronous oscillations via recurrent interactions of STN and GPe neurons. Furthermore, we show that cortical excitatory input to the STN can amplify or suppress pathological STN oscillations depending on their phase and strength, predicting conditions of cortical inputs to the STN for suppressing oscillations.