Miracle-dz/UniFAR-FTUs huggingface dataset:
Fourier Transform Infrared with Attenuated Total Reflectance Applied to the Discrimination of Freshwater Planktonic Coccoid Green Microalgae

Despite the recent advances on fine taxonomic discrimination in microorganisms, namely using molecular biology tools, some groups remain particularly problematic. Fine taxonomy of green algae, a widely distributed group in freshwater ecosystems, remains a challenge, especially for coccoid forms. In this paper, we propose the use of the Fourier Transform Infrared (FTIR) spectroscopy as part of a polyphasic approach to identify and classify coccoid green microalgae (mainly order Sphaeropleales), using triplicated axenic cultures. The attenuated total reflectance (ATR) technique was tested to reproducibility of IR spectra of the biological material, a primary requirement to achieve good discrimination of microalgal strains. Spectral window selection was also tested, in conjunction with the first derivative treatment of spectra, to determine which regions of the spectrum provided better separation and clustering of strains. The non-metric multidimensional scaling (NMDS), analysis of similarities (ANOSIM) and hierarchical clusters (HCA), demonstrated a correct discrimination and classification of closely related strains of chlorophycean coccoid microalgae, with respect to currently accepted classifications. FTIR-ATR was highly reproducible, and provided an excellent discrimination at the strain level. The best separation was achieved by analyzing the spectral windows of 1500–1200 cm−1 and 900–675 cm−1, which differs from those used in previously studies for the discrimination of broad algal groups, and excluding spectral regions related to storage compounds, which were found to give poor discrimination. Furthermore, hierarchical cluster analyses have positioned the strains tested into clades correctly, reproducing their taxonomic orders and families. This study demonstrates that FTIR-ATR has great potential to complement classical approaches for fine taxonomy of coccoid green microalgae, though a careful spectrum region selection is needed.
Cognitive Impairment in Myotonic Dystrophy Type 1 Is Associated with White Matter Damage

Objective To investigate grey (GM) and white matter (WM) abnormalities and their effects on cognitive and behavioral deficits in a large, phenotypically and genotypically well-characterized cohort of classic adult (aDM1, age at onset ≥20 years) or juvenile (jDM1, age at onset <20 years) patients with myotonic dystrophy type 1 (DM1). Methods A case-control study including 51 DM1 patients (17 jDM1 and 34 aDM1) and 34 controls was conducted at an academic medical center. Clinical, cognitive and structural MRI evaluations were obtained. Quantitative assessments of regional GM volumes, WM hyperintensities (WMHs), and microstructural WM tract damage were performed. The association between structural brain damage and clinical and cognitive findings was assessed. Results DM1 patients showed a high prevalence of WMHs, severe regional GM atrophy including the key nodes of the sensorimotor and main cognitive brain networks, and WM microstructural damage of the interhemispheric, corticospinal, limbic and associative pathways. WM tract damage extends well beyond the focal WMHs. While aDM1 patients had severe patterns of GM atrophy and WM tract damage, in jDM1 patients WM abnormalities exceeded GM involvement. In DM1, WMHs and microstructural damage, but not GM atrophy, correlated with cognitive deficits. Conclusions WM damage, through a disconnection between GM structures, is likely to be the major contributor to cognitive impairment in DM1. Our MRI findings in aDM1 and jDM1 patients support the hypothesis of a degenerative (premature aging) origin of the GM abnormalities and of developmental changes as the principal substrates of microstructural WM alterations in DM1.
Applying the New Institute for Healthcare Improvement Inpatient Waste Tool to Identify “Waste” in the Intensive Care Unit

Abstract:Healthcare waste—the inappropriate use of healthcare resources that provides no benefit to patients yet contributes to cost and even harm—is a potentially significant contributor to high healthcare costs. This project aimed to apply a new locally modified Institute for Healthcare Improvement (IHI)–developed waste identification tool to measure the prevalence of and reason for the inappropriate use of intensive care unit (ICU) beds, one type of potential waste. Unnecessary days (i.e., waste) and their causes in a 16-bed “closed” medical ICU (MICU) and a 10-bed “semi-closed” transplant surgical ICU (TSICU) were identified by physicians over a 3-month period. Data on 513 patients admitted to both ICUs for a total of 1,631 patient-days demonstrated that 15% of MICU days and 25.8% of TSICU days were unnecessary. Although causes of waste in each ICU differed, delays in transfer of patients out of the ICU, end-of-life decision-making, and delays in procedures were among the commonest. Determination of waste also varied among physicians, ranging from 4.5% to 27.7% in the MICU and 0%–37.5% in the TSICU. This study found that the IHI waste tool can be effectively used to identify waste in the ICU, which is common and varies based on the ICU type and physician perceptions.
Identification and Validation of a Diagnostic and Prognostic Multi-Gene Biomarker Panel for Pancreatic Ductal Adenocarcinoma

Late diagnosis and systemic dissemination essentially contribute to the invariably poor prognosis of pancreatic ductal adenocarcinoma (PDAC). Therefore, the development of diagnostic biomarkers for PDAC are urgently needed to improve patient stratification and outcome in the clinic. By studying the transcriptomes of independent PDAC patient cohorts of tumor and non-tumor tissues, we identified 81 robustly regulated genes, through a novel, generally applicable meta-analysis. Using consensus clustering on co-expression values revealed four distinct clusters with genes originating from exocrine/endocrine pancreas, stromal and tumor cells. Three clusters were strongly associated with survival of PDAC patients based on TCGA database underlining the prognostic potential of the identified genes. With the added information of impact of survival and the robustness within the meta-analysis, we extracted a 17-gene subset for further validation. We show that it did not only discriminate PDAC from non-tumor tissue and stroma in fresh-frozen as well as formalin-fixed paraffin embedded samples, but also detected pancreatic precursor lesions and singled out pancreatitis samples. Moreover, the classifier discriminated PDAC from other cancers in the TCGA database. In addition, we experimentally validated the classifier in PDAC patients on transcript level using qPCR and exemplify the usage on protein level for three proteins (AHNAK2, LAMC2, TFF1) using immunohistochemistry and for two secreted proteins (TFF1, SERPINB5) using ELISA-based protein detection in blood-plasma. In conclusion, we present a novel robust diagnostic and prognostic gene signature for PDAC with future potential applicability in the clinic.
An Experimental Study on the Performance and Fairness of Loss Differentiation for TCP

This paper investigates the performance and fairness of receiver-based loss differentiation for TCP. Experimentshave been performed with a FreeBSD kernel implementation. As expected, the results verify theeffectiveness of receiver-based loss differentiation when corruption losses are present. However, if the the corruptinglink is shared with users that do not employ loss differentiation, the performance gain typically comesat the expense of increased unfairness. The results show that a single loss differentiating user may in somecases reduce the bandwidth of users without loss differentiation with up to 35 percent, but there are also cases where loss differentiation has limited fairness implications. The results further show that if a user employs multiple TCP connections over the corrupting link the negative effects of corruption losses are reduced. This is true even if all connections employ regular TCP. Hence, multiple connections at the application level can to some extent be used as a simple mechanism to limit the impact of corruption losses.
Factors determining outcomes in adult patient undergoing mechanical ventilation: A “real-world” retrospective study in an Indian Intensive Care Unit

Background: Characteristics of patients admitted to intensive care units with respiratory failure (RF) and undergoing mechanical ventilation (MV) have been described for particular indications and diseases, but there are few studies in the general Intensive Care Unit (ICU) population and even lesser from developing countries. Objective: This study aims to study clinical characteristics, outcomes, and factors affecting outcomes in adult patients with RF on MV admitted to ICU. Methods: A retrospective study of medical records of all patients admitted to ICU between January 1, 2015, and March 31, 2016. Patients receiving MV for more than 6 h were included in the study. Patients younger than 12 years were excluded. Data were recorded of all patients receiving MV during this period regarding demographics, indications for MV, type and characteristics of ventilation, concomitant complications and treatment, and outcomes. Data were recorded at the initiation of MV and daily all throughout the course of MV. The main outcome measure was all-cause mortality at the end of ICU stay. Results: Of the 500 patients admitted to the ICU during the period of the study, a total of 122 patients received MV (and were included in study) for mean (standard deviation [SD]) duration of 4 (3.4) days. The mean (SD) stay in ICU and hospital was 4.49 (3.52) and 6.4 (3.6), respectively. Overall mortality for the unselected general ICU patients on MV was 67.21% while that for ARDS patients was 76.1%. The main factors independently associated with increased mortality were (i) pre-MV factors: age, Apache II scores, heart failure (odds ratio [OR], 1.42; 95% confidence interval [CI], 0.54–3.73; P < 0.001); (ii) patient management factors: positive end-expiratory pressure (OR, 2.69; 95% CI, 0.84–8.61; P < 0.001); (iii) Factors occurring over the course of MV: PaO2/FiO2ratio < 100 (OR, 1.66; 95% CI, 0.67–4.11; P < 0.001) and development of renal failure (OR, 2.33; 95% CI, 2.05–2.42; P < 0.001) and hepatic failure (OR, 2.07; 95% CI, 1.91–2.24; P < 0.001) after initiation of MV. Conclusions: Outcomes of patients undergoing MV are dependent on various factors (including patient demographics, nature of associated morbidity, characteristics of the MV received, and conditions developing over course of MV) and these factors may be present before or develop after initiation of MV.
Removing piston-driven mechanical chest compression artefacts from the ECG

Piston-driven mechanical chest compression (CC) devices induce a quasi-periodic artefact in the ECG, making rhythm diagnosis unreliable. Data from 230 out-of-hospital cardiac arrest (OHCA) patients were collected in which CCs were delivered using the piston driven LUCAS-2 device. Underlying rhythms were annotated by expert reviewers in artefact-free intervals. Two artefact removal methods (filters) were introduced: a static solution based on Goertzel's algorithm, and an adaptive solution based on a Recursive Least Squares (RLS) filter. The filtered ECG was diagnosed by a shock/no-shock decision algorithm used in a commercial defibrillator and compared with the rhythm annotations. Filter performance was evaluated in terms of balanced accuracy (BAC), the mean of sensitivity (shockable) and specificity (nonshockable). Compared to the unfiltered signal, the static filter increased BAC by 20 points, and the RLS filter by 25 points. Adaptive filtering results in 99.0% sensitivity and 87.3% specificity.
5G Radio Network Design for Ultra-Reliable Low-Latency Communication

5G is currently being standardized and addresses, among other things, new URLLC services. These are characterized by the need to support reliable communication, where successful data transmission can be guaranteed within low latency bounds, like 1 ms, at a low failure rate. This article describes the functionality of both the NR and LTE radio interfaces to provide URLLC services. Achievable latency bounds are evaluated, and the expected spectral efficiency is demonstrated. It is shown that both NR and LTE can fulfill the ITU 5G requirements on URLLC; however, this comes at the cost of reduced spectral efficiency compared to mobile broadband services without latency or reliability constraints. Still, the impact on the overall network performance is expected to be moderate.
Evolutionary Diversification of Insect Innexins

Abstract Phylogenetic analysis of insect innexins supported the hypothesis that six major clades of insect innexins arose by gene duplication prior to the origin of the endopterygote insects. Within one of the six clades (the Zpg Clade), two independent gene duplication events were inferred to have occurred in the lineage of Drosophila , after the most recent common ancestor of the dipteran families Culicidae and Drosophilidae. The relationships among this clades were poorly resolved, except for a sister relationship between ShakB and Ogre. Gene expression data from FlyAtlas supported the hypothesis that the latter gene duplication events gave rise to functional differentiation, with Zpg showing a high level of expression in ovary, and Inx5 and Inx6 showing a high level of expression in testis. Because unduplicated members of this clade in Bombyx mori and Anopheles gambiae showed high levels of expression in both ovary and tests, the expression patterns of the Drosophila members of this clade provide evidence of subdivision of an ancestral gene function after gene duplication.
SHARPIN Is Essential for Cytokine Production, NF-κB Signaling, and Induction of Th1 Differentiation by Dendritic Cells

Spontaneous mutations of the Sharpin (SHANK-associated RH domain-interacting protein, other aliases: Rbckl1, Sipl1) gene in mice result in systemic inflammation that is characterized by chronic proliferative dermatitis and dysregulated secretion of T helper1 (Th1) and Th2 cytokines. The cellular and molecular mechanisms underlying this inflammatory phenotype remain elusive. Dendritic cells may contribute to the initiation and progression of the phenotype of SHARPIN-deficient mice because of their pivotal role in innate and adaptive immunity. Here we show by flow cytometry that SHARPIN- deficiency did not alter the distribution of different DC subtypes in the spleen. In response to TOLL-like receptor (TLR) agonists LPS and poly I:C, cultured bone marrow-derived dendritic cells (BMDC) from WT and mutant mice exhibited similar increases in expression of co-stimulatory molecules CD40, CD80, and CD86. However, stimulated SHARPIN-deficient BMDC had reduced transcription and secretion of pro-inflammatory mediators IL6, IL12P70, GMCSF, and nitric oxide. Mutant BMDC had defective activation of NF-κB signaling, whereas the MAPK1/3 (ERK1/2) and MAPK11/12/13/14 (p38 MAP kinase isoforms) and TBK1 signaling pathways were intact. A mixed lymphocyte reaction showed that mutant BMDC only induced a weak Th1 immune response but stimulated increased Th2 cytokine production from allogeneic naïve CD4+ T cells. In conclusion, loss of Sharpin in mice significantly affects the immune function of DC and this may partially account for the systemic inflammation and Th2-biased immune response.
A Unifying Contrast Maximization Framework for Event Cameras, with Applications to Motion, Depth, and Optical Flow Estimation

We present a unifying framework to solve several computer vision problems with event cameras: motion, depth and optical flow estimation. The main idea of our framework is to find the point trajectories on the image plane that are best aligned with the event data by maximizing an objective function: the contrast of an image of warped events. Our method implicitly handles data association between the events, and therefore, does not rely on additional appearance information about the scene. In addition to accurately recovering the motion parameters of the problem, our framework produces motion-corrected edge-like images with high dynamic range that can be used for further scene analysis. The proposed method is not only simple, but more importantly, it is, to the best of our knowledge, the first method that can be successfully applied to such a diverse set of important vision tasks with event cameras.
A Self-calibrating current-steering 12-bit DAC based on new 1-bit self-test scheme

- This paper presents a self-test self-correction scheme for segmented current steering (CS) DACs. Prior art is critically analyzed. The new scheme improves the DAC linearity by improving the accuracy of the thermometer current sources. The algorithm, which controls the scheme, is described in details. A 12-bit CS DAC, with 6-6 segmentation, is implemented using the new scheme and algorithm. The DAC core is designed with 10-bit intrinsic linearity and this is improved to 12-bit level via self-calibration. High-level simulation results and the CMOS layout of the DAC are presented. Further enhancements of the scheme are suggested.
Restoration of quality degraded image by atmospheric scattering model

The Quality of image is very important when we look at the image. Image quality is degraded by numerous factors when an image is taken. To compensate for degradation, constantly studying the improvement of image quality in image signal processing. In this paper, we propose a method for restoring the quality of images attenuated by the atmospheric scattering model. The degradation of image quality due to to the atmospheric scattering model is caused by phenomena such as fog and smog. This phenomenon can be regarded as a form in which noise having a different concentration is stuck in the entire image. To restore image, we generate a narrow dynamic range using. And then, wide dynamic algorithm is applied. As a result of simulation, we confirmed that this method is effective for images degraded by atmospheric scattering model.
THREE-DIMENSIONAL FINITE ELEMENT ANALYSIS FOR DIFFERENT IMPLANT DIAMETERS

This study was directed to use the Three Dimensional Finite Element Method (ABAQUS software) to analyze the stress distribution pattern of several implant diameters (3.4, 3.9, 4.4 mm). The tested implant was housed in different bone thickness sections (8, 12, 16 mm) modeled as a trabecular core surrounded by a 1.5 mm layer of cortical bone with the mesial and distal section planes not covered by cortical bone.
Online Abuse of UK MPs in 2015 and 2017: Perpetrators, Targets, and Topics

Concerns have reached the mainstream about how social media are affecting political outcomes. One trajectory for this is the exposure of politicians to online abuse. In this paper we use 1.4 million tweets from the months before the 2015 and 2017 UK general elections to explore the abuse directed at politicians. This collection allows us to look at abuse broken down by both party and gender and aimed at specific Members of Parliament. It also allows us to investigate the characteristics of those who send abuse and their topics of interest. Results show that in both absolute and proportional terms, abuse increased substantially in 2017 compared with 2015. Abusive replies are somewhat less directed at women and those not in the currently governing party. Those who send the abuse may be issue-focused, or they may repeatedly target an individual. In the latter category, accounts are more likely to be throwaway. Those sending abuse have a wide range of topical triggers, including borders and terrorism.
The Drosophila TGF-beta/Activin-like ligands Dawdle and Myoglianin appear to modulate adult lifespan through regulation of 26S proteasome function in adult muscle

ABSTRACT The Drosophila Activin signaling pathway employs at least three separate ligands – Activin-β (Actβ), Dawdle (Daw), and Myoglianin (Myo) – to regulate several general aspects of fruit fly larval development, including cell proliferation, neuronal remodeling, and metabolism. Here we provide experimental evidence indicating that both Daw and Myo are anti-ageing factors in adult fruit flies. Knockdown of Myo or Daw in adult fruit flies reduced mean lifespan, while overexpression of either ligand in adult muscle tissues but not in adipose tissues enhanced mean lifespan. An examination of ubiquitinated protein aggregates in adult muscles revealed a strong inverse correlation between Myo- or Daw-initiated Activin signaling and the amount of ubiquitinated protein aggregates. We show that this correlation has important functional implications by demonstrating that the lifespan extension effect caused by overexpression of wild-type Daw or Myo in adult muscle tissues can be completely abrogated by knockdown of a 26S proteasome regulatory subunit Rpn1 in adult fly muscle, and that the prolonged lifespan caused by overexpression of Daw or Myo in adult muscle could be due to enhanced protein levels of the key subunits of 26S proteasome. Overall, our data suggest that Activin signaling initiated by Myo and Daw in adult Drosophila muscles influences lifespan, in part, by modulation of protein homeostasis through either direct or indirect regulation of the 26S proteasome levels. Since Myo is closely related to the vertebrate muscle mass regulator Myostatin (GDF8) and the Myostatin paralog GDF11, our observations may offer a new experimental model for probing the roles of GDF11/8 in ageing regulation in vertebrates. This article has an associated First Person interview with the first author of the paper. Summary: This article has, for the first time, demonstrated that fruit fly TGF-beta, or Activin-type ligand Daw, or Myo-initiated Activin signaling in adult fruit fly muscle tissues works as an anti-ageing factor by regulating 26S proteasome activities in those tissues.
Planning, optimisation and evaluation of hyperthermia treatments

Abstract Background: Hyperthermia treatment planning using dedicated simulations of power and temperature distributions is very useful to assist in hyperthermia applications. This paper describes an advanced treatment planning software package for a wide variety of applications. Methods: The in-house developed C++ software package Plan2Heat runs on a Linux operating system. Modules are available to perform electric field and temperature calculations for many heating techniques. The package also contains optimisation routines, post-treatment evaluation tools and a sophisticated thermal model enabling to account for 3D vasculature based on an angiogram or generated artificially using a vessel generation algorithm. The use of the software is illustrated by a simulation of a locoregional hyperthermia treatment for a pancreatic cancer patient and a spherical tumour model heated by interstitial hyperthermia, with detailed 3D vasculature included. Results: The module-based set-up makes the software flexible and easy to use. The first example demonstrates that treatment planning can help to focus the heating to the tumour. After optimisation, the simulated absorbed power in the tumour increased with 50%. The second example demonstrates the impact of accurately modelling discrete vasculature. Blood at body core temperature entering the heated volume causes relatively cold tracks in the heated volume, where the temperature remains below 40 °C. Conclusions: A flexible software package for hyperthermia treatment planning has been developed, which can be very useful in many hyperthermia applications. The object-oriented structure of the source code allows relatively easy extension of the software package with additional tools when necessary for future applications.