julilili42/papers huggingface dataset:
Computational Models of Human Decision-Making with Application to the Internet of Everything
2020-11-23

The concept of the Internet of Things (IoT) first appeared a few decades ago. Today, by the ubiquitous wireless connectivity, the boost of machine learning and artificial intelligence, and the advances in big data analytics, it is safe to say that IoT has evolved to a new concept called the Internet of Everything (IoE) or the Internet of All. IoE has four pillars: Things, human, data, and processes, which render it as an inhomogeneous large-scale network. A crucial challenge of such a network is to develop management, analysis, and optimization policies that besides utility-maximizer machines, also take irrational humans into account. We discuss several networking applications in which appropriate modeling of human decision-making is vital. We then provide a brief review of computational models of human decision-making. Based on one such model, we develop a solution for a task offloading problem in fog computing and we analyze the implications of including humans in the loop.
T2-Pseudonormalization and Microstructural Characterization in Advanced Stages of Late-infantile Metachromatic Leukodystrophy
2020-11-23

Abstract Purpose T2-weighted signal hyperintensities in white matter (WM) are a diagnostic finding in brain magnetic resonance imaging (MRI) of patients with metachromatic leukodystrophy (MLD). In our systematic investigation of the evolution of T2-hyperintensities in patients with the late-infantile form, we describe and characterize T2-pseudonormalization in the advanced stage of the natural disease course. Methods The volume of T2-hyperintensities was quantified in 34 MRIs of 27 children with late-infantile MLD (median age 2.25 years, range 0.5–5.2 years). In three children with the most advanced clinical course (age &gt;4 years) and for whom the T2-pseudonormalization was the most pronounced, WM microstructure was investigated using a multimodal MRI protocol, including diffusion-weighted imaging, MR spectroscopy (MRS), myelin water fraction (MWF), magnetization transfer ratio (MTR), T1-mapping and quantitative susceptibility mapping. Results T2-hyperintensities in cerebral WM returned to normal in large areas of 3 patients in the advanced disease stage. Multimodal assessment of WM microstructure in areas with T2-pseudonormalization revealed highly decreased values for NAA, neurite density, isotropic water, mean and radial kurtosis, MWF and MTR, as well as increased radial diffusivity. Conclusion In late-infantile MLD patients, we found T2-pseudonormalization in WM tissue with highly abnormal microstructure characterizing the most advanced disease stage. Pathological hallmarks might be a loss of myelin, but also neuronal loss as well as increased tissue density due to gliosis and accumulated storage material. These results suggest that a multimodal MRI protocol using more specific microstructural parameters than T2-weighted sequences should be used when evaluating the effect of treatment trials in MLD.
Right-sided infective endocarditis in association with a left-to-right shunt complicated by haemoptysis and acute renal failure: a case report
2020-11-23

Abstract Background Infective endocarditis has a relevant clinical impact due to its high morbidity and mortality rates. Right-sided endocarditis has lower complication rates than left-sided endocarditis. Common complications are multiple septic pulmonary embolisms, haemoptysis, and acute renal failure. Risk factors associated with right-sided infective endocarditis are commonly related to intravenous drug abuse, central venous catheters, or infections due to implantable cardiac devices. However, patients with congenital ventricular septal defects might be at high risk of endocarditis and haemodynamic complications. Case presentation In the following, we present the case of a 23-year-old man without a previous intravenous drug history with tricuspid valve Staphylococcus aureus endocarditis complicated by acute renal failure and haemoptysis caused by multiple pulmonary emboli. In most cases, right-sided endocarditis is associated with several common risk factors, such as intravenous drug abuse, a central venous catheter, or infections due to implantable cardiac devices. In this case, we found a small perimembranous ventricular septal defect corresponding to a type 2 Gerbode defect. This finding raised the suspicion of a congenital ventricular septal defect complicated by a postendocarditis aneurysmal transformation. Conclusions Management of the complications of right-sided infective endocarditis requires a multidisciplinary approach. Echocardiographic approaches should include screening for ventricular septal defects in patients without common risk factors for tricuspid valve endocarditis. Patients with undiagnosed congenital ventricular septal defects are at high risk of infective endocarditis. Therefore, endocarditis prophylaxis after dental procedures and/or soft-tissue infections is highly recommended. An acquired ventricular septal defect is a very rare complication of infective endocarditis. Surgical management of small ventricular septal defects without haemodynamic significance is still controversial.
Paxilline Prevents the Onset of Myotonic Stiffness in Pharmacologically Induced Myotonia: A Preclinical Investigation
2020-11-23

Reduced Cl − conductance causes inhibited muscle relaxation after forceful voluntary contraction due to muscle membrane hyperexcitability. This represents the pathomechanism of myotonia congenita. Due to the prevailing data suggesting that an increased potassium level is a main contributor, we studied the effect of a modulator of a big conductance Ca 2+ - and voltage-activated K + channels (BK) modulator on contraction and relaxation of slow- and high-twitch muscle specimen before and after the pharmacological induction of myotonia. Human and murine muscle specimens (wild-type and BK −/− ) were exposed to anthracene-9-carboxylic acid (9-AC) to inhibit CLC-1 chloride channels and to induce myotonia in-vitro . Functional effects of BK-channel activation and blockade were investigated by exposing slow-twitch (soleus) and fast-twitch (extensor digitorum longus) murine muscle specimens or human musculus vastus lateralis to an activator (NS1608) and a blocker (Paxilline), respectively. Muscle-twitch force and relaxation times (T 90/10 ) were monitored. Compared to wild type, fast-twitch muscle specimen of BK −/− mice resulted in a significantly decreased T 90/10 in presence of 9-AC. Paxilline significantly shortened T 90/10 of murine slow- and fast-twitch muscles as well as human vastus lateralis muscle. Moreover, twitch force was significantly reduced after application of Paxilline in myotonic muscle. NS1608 had opposite effects to Paxilline and aggravated the onset of myotonic activity by prolongation of T 90/10 . The currently used standard therapy for myotonia is, in some individuals, not very effective. This in vitro study demonstrated that a BK channel blocker lowers myotonic stiffness and thus highlights its potential therapeutic option in myotonia congenital (MC).
Enhanced IgG1‐mediated antibody response towards thymus‐dependent immunization in CXCR1‐deficient mice
2020-11-23

Abstract Background Chemokine receptors and their corresponding ligands are key players of immunity by regulation of immune cell differentiation and migration. CXCR1 is a high‐affinity receptor for CXCL8. Differential expression of CXCR1 is associated with a variety of human pathologies including cancer and inflammatory diseases. While various studies have highlighted the importance of CXCR1‐mediated CXCL8‐sensing for neutrophil trafficking and function, its role in B‐cell responses remains unsolved. Therefore, our aim was to investigate innate and adaptive antibody responses in CXCR1‐deficient mice. Methods Cell populations of the spleen and the peritoneal cavity were identified and quantified via flow cytometry. To investigate thymus‐independent (TI) and thymus‐dependent (TD) antibody responses, mice were immunized intraperitoneally with TNP‐Ficoll, Pneumovax23, and TNP‐Chicken Gamma Globulin. Mice were bled before as well as 7 and 14 days after vaccination to collect serum. Serum antibody levels overtime were analyzed according to their specificity by enzyme‐linked immunosorbent assay. B‐1 cell functionality was examined by IL‐5/IL‐5Rα‐dependent stimulation of peritoneal and splenic cells in vitro. To analyze CXCR1/2‐expression, CD19 + splenocytes were enriched by magnetic‐activated cell sorting before isolation of total RNA contents, followed by reverse transcription and real‐time polymerase chain reaction. Results The distribution of natural B‐1 cell populations was disturbed in the absence of CXCR1, while their responsiveness towards TI antigens and in vitro stimulation remained functional. Besides, CXCR1‐deficiency was accompanied by increased frequencies of follicular B‐2 cells in the spleen. Interestingly, these mice produced elevated levels of antigen‐specific IgG 1 upon TD immunization and harbored a significantly enlarged proportion of CXCR5‐expressing T helper (H) cells. CXCR1‐expression was detectable in CD19 + splenocytes derived from wild‐type, but not CXCR1‐deficient mice. Conclusion Our data demonstrate a previously unknown relevance of CXCR1 for the production of specific IgG 1 in response to vaccination. These findings identify CXCR1 as a promising candidate for future studies on the regulation of adaptive antibody responses.
Problems in measuring the JTC-bias in patients with psychotic disorders with the fish task: a secondary analysis of a baseline assessment of a randomized controlled trial
2020-11-23

Abstract Background The jumping to conclusions bias (JTC) is considered to be an important causal factor in theoretical models for the formation and maintenance of delusions. However, recent meta-analytic findings show a rather equivocal pattern of results regarding associations between JTC and delusions. Thus, the present study aims to investigate in a large sample whether the JTC-bias is more pronounced in patients with psychotic disorders in comparison to controls and whether the JTC bias is associated with a more severe delusional conviction, persecutory delusions, and positive symptoms in general. Methods Patients with psychotic disorders ( n = 300) enrolled in a therapy trial and healthy controls ( n = 51) conducted a variant of the beads task (fish task) as a measure for the JTC-bias at the start of the trial. Further, clinical interviews were used to assess patients’ delusional severity and delusional conviction. Results There were no statistically significant differences between patients with psychotic disorders (with 53% displaying the JTC-bias) and controls (41%). Furthermore, there were no statistically significant correlations between JTC measures and persecutory delusions, delusional conviction, and positive symptoms. Conclusions We found no differences in JTC between patients with psychotic disorders and healthy controls, which is in part in line with meta-analytic findings using a wide range of JTC task variants. Interestingly, patients with psychotic disorders displayed JTC rates commonly found in the literature, while healthy control subjects showed an unexpectedly high level of JTC. The task variant we used in the present study (fish task) is discussed as a potential reason for our results, as it may induce a more deliberative reasoning style in controls as compared to the traditional beads task. Furthermore, possible implications for the measurement of the JTC-bias, in general, are discussed. Trial Registration ISRCTN29242879 ( isrctn.com ), date of registration: April 12th 2006, retrospectively registered.
MiR-9 and the Midbrain-Hindbrain Boundary: A Showcase for the Limited Functional Conservation and Regulatory Complexity of MicroRNAs
2020-11-23

MicroRNAs regulate gene expression at post-transcriptional levels. Some of them appear to regulate brain development and are involved in neurodevelopmental disorders. This has led to the suggestion that the role of microRNAs in neuronal development and function may be more central than previously appreciated. Here, we review the data about miR-9 function to depict the subtlety, complexity, flexibility and limited functional conservation of this essential developmental regulatory system. On this basis we propose that species-specific actions of miR-9 could underlie to a large degree species differences in brain size, shape and function.
Near-optimal rotation of colour space by zebrafish cones in vivo
2020-11-23

<title>Abstract</title> For colour vision, retinal circuits must separate information about intensity and wavelength. This requires circuit-level comparison of at least two spectrally distinct photoreceptors. However, many vertebrates use four or more, and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture and function of outer retinal circuits underlying colour processing in the tetrachromatic larval zebrafish. Our findings reveal that the specific spectral tunings of the four cone types near optimally rotate the encoding of natural daylight in a principal component analysis (PCA)-like manner to yield one primary achromatic axis, two colour-opponent axes as well as a secondary UV-achromatic axis for prey capture. We note that fruit flies – the only other tetrachromat species where comparable circuit-level information is available - use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into achromatic and chromatic axes at the eye’s first synapse may be a fundamental principle of colour vision when using more than two spectrally well-separated photoreceptor types.
Audio files for A Dataset of EEG and EOG recordings from an Auditory EOG-based Communication System for Patients in Locked-In State
2020-11-23

&lt;ol&gt; &lt;li&gt;Origin of the data&lt;/li&gt; &lt;/ol&gt; &lt;p&gt;These Audio files are related to the publication &quot;A dataset of EEG and EOG from an auditory EOG-based communication system for patients in locked-in state&quot; by Andres Jaramillo-Gonzalez, Shize Wu, Alessandro Tonin, Aygul Rana, Majid Khalili-Ardali, Niels Birbaumer, and Ujwal Chaudhary. To use the audio data, please contact&nbsp; Dr. Ujwal Chaudhary, as mentioned in the manuscript.&lt;/p&gt; &lt;ol&gt; &lt;li&gt;Details of the data&lt;/li&gt; &lt;/ol&gt; &lt;p&gt;The description of the nature and details of the *.txt files are in the section &quot;Data Records&quot; of the manuscript. As mentioned in the manuscript, before the beginning of the study, at least 100 questions with known &quot;yes&quot; or &quot;no&quot; answers were formulated and recorded with a family member or caretaker&#39;s voice close to the patient.&nbsp; Each question with a &quot;yes&quot; answer is paired with a similar question with a &quot;no&quot; answer (e.g., &quot;Paris is the capital of France&quot; and &quot;Berlin is the capital of France&quot;).&lt;/p&gt; &lt;p&gt;Each question is saved as an audio file with an explicit identifier, a question with a &quot;yes&quot; answer is saved with a 001_NUMBER identifier, and a question with a &quot;no&quot; answer is saved with a 002_NUMBER identifier. The NUMBER label is composed of 5 digits; the first two determine the number of the patient, and the last three digits indicate the number of the question. The value of the label NUMBER is the same for a semantically paired sentence. In the example, &quot;001_11007.wav&quot; indicates a &quot;yes&quot; type of answer, question number 07 from P11. Sentences are then placed in a specific folder of the used laptop&#39;s storage, accessed and played by the communication system along with the sessions during sentence presentation.&lt;/p&gt;
Audio files for A Dataset of EEG and EOG recordings from an Auditory EOG-based Communication System for Patients in Locked-In State
2020-11-23

Origin of the data These Audio files are related to the publication "A dataset of EEG and EOG from an auditory EOG-based communication system for patients in locked-in state" by Andres Jaramillo-Gonzalez, Shize Wu, Alessandro Tonin, Aygul Rana, Majid Khalili-Ardali, Niels Birbaumer, and Ujwal Chaudhary. To use the audio data, please contact Dr. Ujwal Chaudhary, as mentioned in the manuscript. Details of the data The description of the nature and details of the *.txt files are in the section "Data Records" of the manuscript. As mentioned in the manuscript, before the beginning of the study, at least 100 questions with known "yes" or "no" answers were formulated and recorded with a family member or caretaker's voice close to the patient. Each question with a "yes" answer is paired with a similar question with a "no" answer (e.g., "Paris is the capital of France" and "Berlin is the capital of France"). Each question is saved as an audio file with an explicit identifier, a question with a "yes" answer is saved with a 001_NUMBER identifier, and a question with a "no" answer is saved with a 002_NUMBER identifier. The NUMBER label is composed of 5 digits; the first two determine the number of the patient, and the last three digits indicate the number of the question. The value of the label NUMBER is the same for a semantically paired sentence. In the example, "001_11007.wav" indicates a "yes" type of answer, question number 07 from P11. Sentences are then placed in a specific folder of the used laptop's storage, accessed and played by the communication system along with the sessions during sentence presentation.
Hypothyroidism Increases Cholesterol Gallstone Prevalence in Mice by Elevated Hydrophobicity of Primary Bile Acids
2020-11-24

<b><i>Background:</i></b> Thyroid hormone (TH) deficiency has been associated with increased cholesterol gallstone prevalence. Hypothyroidism impacts hepatic lipid homeostasis, biliary secretion, gallbladder motility, and gallstone (LITH) gene expression, all potential factors contributing to cholesterol gallstone disease (CGD). However, how TH deficiency may lead to gallstone formation is still poorly understood. Therefore, we performed molecular studies in a CGD mouse model under lithogenic conditions and modulation of TH status. <b><i>Methods:</i></b> Male, three-month-old C57BL/6 mice were randomly divided into a control (euthyroid) group, a hypothyroid (hypo) group, a gallstone (litho) group, and a gallstone+hypothyroid (litho+hypo) group and were treated for 2, 4, and 6 weeks (<i>n</i> = 8/treatment period). Gallstone prevalence, biliary composition and cholesterol crystals, hepatic expression of genes participating in cholesterol, bile acid (BA), and phosphatidylcholine synthesis (<i>Hmgcr</i>, <i>Cyp7a1</i>, <i>Pcyt1a</i>), and canalicular transport (<i>Abcg5</i>, <i>Bsep</i>, <i>Abcb4</i>) were investigated. <b><i>Results:</i></b> Increased cholesterol gallstone prevalence was observed in hypothyroid mice under lithogenic diet after 4 and 6 weeks of treatment (4 weeks: 25% vs. 0%; 6 weeks: 75% vs. 37.5%). Interestingly, neither the composition of the three main biliary components, cholesterol, BAs, and phosphatidylcholine, nor the hepatic expression of genes involved in synthesis and transport could explain the differences in cholesterol gallstone formation in the mice. However, TH deficiency resulted in significantly increased hydrophobicity of primary BAs in bile. Furthermore, downregulation of hepatic sulfonation enzymes <i>Papss2</i> and <i>Sult2a8</i> as well as diminished biliary BA sulfate concentrations in mice were observed under hypothyroid conditions all contributing to a lithogenic biliary milieu as evidenced by microscopic cholesterol crystals and macroscopic gallstone formation. <b><i>Conclusions:</i></b> We describe a novel pathogenic link between TH deficiency and CGD and suggest that the increased hydrophobic character of biliary BAs due to the diminished expression of hepatic detoxification enzymes promotes cholesterol crystal precipitation and enhances cholesterol gallstone formation in the bile of hypothyroid mice.
Evaluation of bowel wall thickness by ultrasound as early diagnostic tool for therapeutic response in Crohn’s disease patients treated with ustekinumab
2020-11-24

Abstract Background Ustekinumab was approved for the treatment of patients with moderate to severe CD 2. Development of predictors for selecting patients responding to ustekinumab has to be the next step. US offers a noninvasive method with great sensitivity in detecting CD activity 11. Aim To evaluate BWT by BS as early diagnostic tool for treatment response in CD patients treated with ustekinumab at week 8. Methods This is a prospective monocentric study. Twenty-three CD patients had BS at the time of first and second application. BS was performed by one of 2 experienced DEGUM certificated sonographers, with evaluation by both independently and blindly. Primary endpoint was substantial sonographic response defined as decrease of BWT ≥ 1 mm. Secondary endpoint was concordance between sonographic and clinical response, defined as decrease of CDAI ≥ 70 points and sonographic and biochemical response defined as decrease of CRP ≥ 0.5 mg/dl. Results At week 8, BS detected in 10 of 23 patients a substantial decrease of BWT ≥ 1 mm; in 7, a decrease &lt; 1 mm. Compared to baseline, all 17 patients showed generally improved blood data and 16/17 generally improved clinical data. Of those with a decrease of BWT ≥ 1 mm, we observed a substantial decrease of CDAI ≥ 70 points in 9/10 patients and a substantial decrease of CRP ≥ 0.5 mg/dl in 8/10 patients. Conclusion Our study suggests that sonographic measurement of BWT can be a helpful parameter for selecting patients responding early to ustekinumab and for providing assistance in terms of further treatment interval at week 8.
Proceedings of the EuBIC-MS 2020 Developers’ Meeting
2020-11-24

The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13th to January 17th 2020 in Nyborg, Denmark. Among the participants were scientists as well as developers working in the field of computational mass spectrometry (MS) and proteomics. The 4-day program was split between introductory keynote lectures and parallel hackathon sessions. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts, and to actively contribute to highly relevant research projects. We successfully produced several new tools that will be useful to the proteomics community by improving data analysis as well as facilitating future research. All keynote recordings are available on https://doi.org/10.5281/zenodo.3890181.
Polymeric dimethylytterbium and the terminal methyl complex (TptBu,Me)Yb(CH3)(thf)
2020-11-24

Pyrophoric redox-sensitive [YbMe<sub>2</sub>]<sub>n</sub>is obtained from [Yb{N(SiMe<sub>3</sub>)<sub>2</sub>}<sub>2</sub>]<sub>2</sub>and methyllithium and its existence proven by<sup>171</sup>Yb CP/MAS NMR spectroscopy and distinct methane elimination reactions.