Miracle-dz/UniFAR-FTUs huggingface dataset:
LncRNAs in molluscan and mammalian stages of parasitic schistosomes are developmentally-regulated and coordinately expressed with protein-coding genes

ABSTRACT Despite the low level expression of some long noncoding RNAs (lncRNAs), the differential expression of specific lncRNAs plays important roles during the development of many organisms. Schistosomes, parasitic flatworms that are responsible for schistosomiasis, infects over 200 million people resulting in chronic disease and hundreds of thousands of deaths. Schistosomes have a complex life cycle that transitions between molluscan and mammalian hosts. In a molluscan snail host, the sporocyst stage develops over 5 weeks undergoing asexual reproduction to give rise to free-swimming and infectious cercariae that penetrate human skin and eventually mature into egg producing worms in mammals. The tight integration of the sporocyst to the snail host hepatopancreas hinders the -omics study in the molluscan stage, so the sporocyst transcriptome has only been examined for lncRNAs in immature in vitro samples. Here we analyzed the in vivo mature sporocyst transcriptome to identify 4,930 total lncRNAs between the molluscan and mammalian stages of the parasite. We further demonstrate that the lncRNAs are differentially expressed in a development-dependent manner. In addition, we constructed a co-expression correlation network between lncRNAs and protein-coding (PC) genes that was used to identify clusters of lncRNA transcripts with potential functional relevance. We also describe lncRNA–lncRNA and lncRNA–kinome correlations that identify lncRNAs with prospective roles in gene regulation. Finally, our results show clear differential expression patterns of lncRNAs in host-dependent development stages of S. mansoni and ascribe potential functional roles in development based on predicted intracellular interaction.
ANALISIS TROMBOSITOPENIA SEBAGAI FAKTOR RISIKO KEMATIAN PASIEN SEPSIS DI RSUDZA BANDA ACEH

Sepsis adalah Systemic Inflammatory Response Syndrome (SIRS) ditambah tempat infeksi yang diketahui. Sepsis merupakan salah satu penyebab utama kematian di seluruh dunia. Respon sistemik akibat proses infeksi menyebabkan aktivasi dari platelet dan supresi sumsum tulang sehingga sering ditemukan trombositopenia pada pasien sepsis. Tujuan dari penelitian ini untuk menganalisis trombositopenia sebagai faktor risiko kematian pasien sepsis di RSUDZA. Penelitian ini merupakan penelitian cohort retrospective dengan menggunakan data sekunder yang diambil melalui rekam medis pasien periode Januari-Desember 2015. Pengambilan sampel dilakukan dengan metode total sampling dan dianalisis dengan uji Chi-Square. Pasien dibagi dalam 2 kategori yaitu trombositopenia dan tanpa trombositopenia. Data penelitian menunjukkan dari 143 pasien didapatkan usia rata-rata pasien 56,87±14,6 tahun dan 46,2% fokus infeksi berasal dari sistem respirasi. Pasien sepsis yang mengalami trombositopenia sebanyak 61 pasien (42,7%) yang mana 48 pasiennya (78,7%) meninggal. Angka kematian pasien sepsis tanpa trombositopenia adalah 50% (RR 1,57; IK 95% 1.22 – 2.03; p = 0.001). Kesimpulan dari penelitian ini yaitu pasien sepsis dengan trombositopenia berisiko mengalami kematian dibanding dengan pasien sepsis tanpa trombositopenia. Kata kunci : Kematian, Sepsis, Trombositopenia
Sensory systems in birds: What we have learned from studying sensory specialists

“Diversity” is an apt descriptor of the research career of Jack Pettigrew as it ranged from the study of trees, to clinical conditions, to sensory neuroscience. Within sensory neuroscience, he was fascinated by the evolution of sensory systems across species. Here, we review some of his work on avian sensory specialists and research that he inspired in others. We begin with an overview of the importance of the Wulst in stereopsis and the need for further study of the Wulst in relation to binocularity across avian species. Next, we summarize recent anatomical, behavioral, and physiological studies on optic flow specializations in hummingbirds. Beyond vision, we discuss the first evidence of a tactile “fovea” in birds and how this led to detailed studies of tactile specializations in waterfowl and sensorimotor systems in parrots. We then describe preliminary studies by Pettigrew of two endemic Australian species, the plains‐wanderer (Pedionomus torquatus) and letter‐winged kite (Elanus scriptus), that suggest the evolution of some unique auditory and visual specializations in relation to their unique behavior and ecology. Finally, we conclude by emphasizing the importance of a comparative and integrative approach to understanding avian sensory systems and provide an example of one system that has yet to be properly examined: tactile facial bristles in birds. Through reviewing this research and offering future avenues for discovery, we hope that others also embrace the comparative approach to understanding sensory system evolution in birds and other vertebrates.
Associations between stopping prescriptions for opioids, length of opioid treatment, and overdose or suicide deaths in US veterans: observational evaluation

Abstract Objective To examine the associations between stopping treatment with opioids, length of treatment, and death from overdose or suicide in the Veterans Health Administration. Design Observational evaluation. Setting Veterans Health Administration. Participants 1 394 102 patients in the Veterans Health Administration with an outpatient prescription for an opioid analgesic from fiscal year 2013 to the end of fiscal year 2014 (1 October 2012 to 30 September 2014). Main outcome measures A multivariable Cox non-proportional hazards regression model examined death from overdose or suicide, with the interaction of time varying opioid cessation by length of treatment (≤30, 31-90, 91-400, and >400 days) as the main covariates. Stopping treatment with opioids was measured as the time when a patient was estimated to have no prescription for opioids, up to the end of the next fiscal year (2014) or the patient’s death. Results 2887 deaths from overdose or suicide were found. The incidence of stopping opioid treatment was 57.4% (n=799 668) overall, and based on length of opioid treatment was 32.0% (≤30 days), 8.7% (31-90 days), 22.7% (91-400 days), and 36.6% (>400 days). The interaction between stopping treatment with opioids and length of treatment was significant (P<0.001); stopping treatment was associated with an increased risk of death from overdose or suicide regardless of the length of treatment, with the risk increasing the longer patients were treated. Hazard ratios for patients who stopped opioid treatment (with reference values for all other covariates) were 1.67 (≤30 days), 2.80 (31-90 days), 3.95 (91-400 days), and 6.77 (>400 days). Descriptive life table data suggested that death rates for overdose or suicide increased immediately after starting or stopping treatment with opioids, with the incidence decreasing over about three to 12 months. Conclusions Patients were at greater risk of death from overdose or suicide after stopping opioid treatment, with an increase in the risk the longer patients had been treated before stopping. Descriptive data suggested that starting treatment with opioids was also a risk period. Strategies to mitigate the risk in these periods are not currently a focus of guidelines for long term use of opioids. The associations observed cannot be assumed to be causal; the context in which opioid prescriptions were started and stopped might contribute to risk and was not investigated. Safer prescribing of opioids should take a broader view on patient safety and mitigate the risk from the patient’s perspective. Factors to address are those that place patients at risk for overdose or suicide after beginning and stopping opioid treatment, especially in the first three months.
Malnutrition among children raises intimidation to their health in Bangladesh: control strategies

Nutritional status of children is a momentous issue across the world. Children are mostly suffering from various infectious diseases, which are ensuing through malnutrition or incommensurable nutritional requirement of children. Household food security, caring practice for women and children, health environment and services and infectious diseases are the major cause of mortality particularly in children in many developing countries. The findings of the review clearly relate malnutrition, which is one of the most underlying causes of infectious diseases among children and existing evidence shows that the prevalence of under-nutrition and other forms of malnutrition among under-five children was high and they are easily affected by infectious disease such as diarrhea, measles, malaria, acute respiratory infection etc.A well-designed social protection system has great potential to improve malnutrition in Bangladesh. The international and domestic evidence presented in this review clearly demonstrates the importance of an integrated approach to tackling malnutrition in Bangladesh. Severe wasting may be reduced by simply improving food intake but tackling chronic malnutrition requires integrated social protection programmes. Programmes that have effectively reduced stunting and wasting have also addressed many of the underlying causes of malnutrition, including improving household food security and the health environment.
A super-quadratic lower bound for depth four arithmetic circuits

We show an Ω(n2.5) lower bound for general depth four arithmetic circuits computing an explicit n-variate degree-Θ(n) multilinear polynomial over any field of characteristic zero. To our knowledge, and as stated in the survey [88], no super-quadratic lower bound was known for depth four circuits over fields of characteristic ≠ 2 before this work. The previous best lower bound is Ω(n1.5) [85], which is a slight quantitative improvement over the roughly Ω(n1.33) bound obtained by invoking the super-linear lower bound for constant depth circuits in [73, 86]. Our lower bound proof follows the approach of the almost cubic lower bound for depth three circuits in [53] by replacing the shifted partials measure with a suitable variant of the projected shifted partials measure, but it differs from [53]'s proof at a crucial step - namely, the way "heavy" product gates are handled. Loosely speaking, a heavy product gate has a relatively high fan-in. Product gates of a depth three circuit compute products of affine forms, and so, it is easy to prune Θ(n) many heavy product gates by projecting the circuit to a low-dimensional affine subspace [53, 87]. However, in a depth four circuit, the second (from the top) layer of product gates compute products of polynomials having arbitrary degree, and hence it was not clear how to prune such heavy product gates from the circuit. We show that heavy product gates can also be eliminated from a depth four circuit by projecting the circuit to a low-dimensional affine subspace, unless the heavy gates together account for ΩT(n2.5) size. This part of our argument is inspired by a well-known greedy approximation algorithm for the weighted set-cover problem.
Out-of-Distribution Detection with Likelihoods Assigned by Deep Generative Models Using Multimodal Prior Distributions

Modern machine learning systems can exhibit undesirable and unpredictable behavior in response to out-of-distribution inputs. Consequently, applying out-of-distribution detection to address this problem is an active subﬁeld of safe AI. Probability density estimation is one popular approach for out-of-distribution detection of low-dimensional data. However, for high dimensional data, recent work has reported that deep generative models can assign higher likelihoods to out-of-distribution data than to training data. We propose a new method to detect out-of-distribution inputs using deep generative models with multimodal prior distributions. Our experimental results show that our models trained on Fashion-MNIST successfully assign lower likelihoods to MNIST, and successfully function as out-of-distribution detectors.
Continuous Safe Learning Based on First Principles and Constraints for Autonomous Driving

We propose a continuous learning system for autonomous driving based on first principles and constraints. The learning system includes a knowledge base to represent the first principles’ manifestations; Initial vehicle control commands are derived from the knowledge base, and constrained exploration and sequence analysis based intelligent exploitation are used to refine the control commands and keep the learning safe. A decomposed learning curriculum is utilized to enrich the knowledge base and handle complicated scenarios. Our experiments in simulations and real test environments show the system’s advantages of fast learning, smooth driving, and quick adapting. The proposed system does not require the complicated vehicle model calibration, and facilitates the easy transfer learning from simulation environments to real driving environments.
Physiologic responses to simulated care activities in older surgical patients

Physiologic Responses to Simulated Care Activities in Older Surgical Patients Older adults often experience loss of function during hospitalization, thus clinical care activities, like transferring, are part of routine hospital care to prevent functional decline. A paucity of research exists to measure this type of activity objectively. This instrument feasibility study evaluated the utility of the ActiheartTM to measure heart rate and motion responses to five activities, turning, dangling, transferring, sitting, and walking. Fifty-four adults aged 65 and older (M=72), scheduled for surgery, participated in a simulation of the five clinical care activities. The study’s major findings indicate that the ActiheartTM: 1) successfully measured motion and heart rate during various activities; 2) worked well to measure activities that may not show much change in motion alone (like sitting) or heart rate alone (like transferring); 3) discriminated between different clinical care activities, some more consistently than others; 4) discriminated heart rate and motion differences within each clinical care activity; and 5) can reasonably measure heart rate and motion even in the presence of covariates such as gender and BMI. This study was the first to explore the utility and feasibility of the ActiheartTM in a cohort of older adults in a hospital-like environment. It should next be used in an inpatient setting to examine activity patterns of older adults during hospitalization. Author: Colleen M. Casey
In Silico Clinical Trials through AI and Statistical Model Checking

A Virtual Patient (VP) is a computational model accounting for individualised (patho-) physiology and Pharmaco-Kinetics/Dynamics of relevant drugs. Availability of VPs is among the enabling technology for In Silico Clinical Trials. Here we shortly outline the state of the art as for VP generation and summarise our recent work on Artiﬁcial Intelligence (AI) and Statistical Model Checking based generation of VPs.
Domino Problem Under Horizontal Constraints

18 The Domino Problem on Z 2 asks if it is possible to tile the plane with a given set of Wang tiles; it 19 is a classical decision problem which is known to be undecidable. The purpose of this article is to 20 parameterize this problem to explore the frontier between decidability and undecidability. To do 21 so we ﬁx horizontal constraints H on the tiles and consider a new Domino Problem DP H : given a 22 vertical constraint, is it possible to tile the plane? We characterize the nearest-neighbor horizontal 23 constraints where DP H is decidable using graphs combinatorics. 24
On Covering Segments with Unit Intervals

We study the problem of covering a set of segments on a line with the minimum number of unit-length intervals, where an interval covers a segment if at least one of the two endpoints of the segment falls in the unit interval. We also study several variants of this problem. We show that the restrictions of the aforementioned problems to the set of instances in which all the segments have the same length are NP-hard. This result implies several NP-hardness results in the literature for variants and generalizations of the problems under consideration. We then study the parameterized complexity of the aforementioned problems. We provide tight results for most of them by showing that they are fixed-parameter tractable for the restrictions in which all the segments have the same length, and are W[1]-complete otherwise. 2012 ACM Subject Classification Theory of computation → Parameterized complexity and exact algorithms; Theory of computation → Computational geometry
Wireless Photoplethysmography Sensor for Continuous Blood Pressure Biosignal Shape Acquisition

Blood pressure assessment plays a vital role in day-to-day clinical diagnosis procedures as well as personal monitoring. Thus, blood pressure monitoring devices must afford convenience and be easy to use with no side effects on the user. This paper presents a compact, economical, power-efficient, and convenient wireless plethysmography sensor for real-time blood pressure biosignal monitoring. The proposed sensor facilitates blood pressure signal shape sensing, signal conditioning, and data conversion as well as its wireless transmission to a monitoring terminal. Received data can, subsequently, be compiled and stored on a computer via a Wi-Fi module. During monitoring, users can observe blood pressure signals being processed and displayed on the graphical user interface (GUI)—developed using a virtual instrumentation (VI) application. The proposed device comprises a finger clip optical pulse sensor, analogue signal preprocessing, microcontroller, and Wi-Fi module. It consumes approximately 500 mW power when operating in the active mode and synthesized using commercial off-the-shelf (COTS) components. Experimental results reveal that the proposed device is reliable and facilitates efficient blood pressure monitoring. The proposed wireless photoplethysmographic (PPG) sensor is a preliminary (or first) version of the intended device manifestation. It provides raw blood pressure data for further classification. Additionally, the collected data concerning the blood pressure wave shape can be easily analysed for use in other biosignal observations, interpretations, and investigations. The design approach also allows the device to be built into a wearable system for further research purposes.
Optimization and Multistage Systems. The Thawing Case

Multistage systems are systems characterized by n stages, where each stage has a precise parametric evolution law. We propose a procedure to reduce the optimal parameter synthesis on a multistage system to the optimal control design on an automaton with a DAG structure that we will call multistage automaton. We describe the procedure using a thawing system as a case study. We address the optimization problem as a reachability problem and we use backtrack strategy to obtain a feasible solution in the linear case.
Dynamic Measurement of Legs Motion in Sagittal Plane Based on Soft Wearable Sensors

Human motion capture is widely used in exoskeleton robots, human-computer interaction, sports analysis, rehabilitation training, and many other fields. However, soft-sensor-based wearable dynamic measurement has not been well achieved. In this paper, the dynamic measurements of legs were investigated by using dielectric elastomers as stain sensors, and an alternating signal was applied to detect the dynamic rotational angles of the legs. To realize a quick response, parameters of the sensors were optimized by circuit analysis. The sensor can detect hip, knee, and ankle joint motions with a sample frequency of 200 Hz. The measurements of the sensors were compared with a commercial motion capture system from PhaseSpace, and dynamic errors between them were smaller than 3° when squatting and walking at low speed and smaller than 5° when walking at high speed. Experiments therefore demonstrate the feasibility of the integrated wearable stretch sensors with pants.
Beyond DBpedia & YAGO - The New Kids on the Knowledge Graph Block

Starting with Cyc in the 1980s [6], the collection of general knowledge in machine interpretable form has been considered a valuable ingredient in intelligent and knowledge intensive applications. Notable contributions in the ﬁeld include the Wikipedia-based datasets DBpe-dia [5] and YAGO [10], as well as the collaborative knowledge base Wikidata [11]. Since Google has coined the term in 2012, they are most often referred to as knowledge graphs [1, 8]. Besides such open knowledge graphs, many companies have started using corporate knowledge graphs as a means of information representation [7]. In this talk, I will look at two ongoing projects related to the extraction of knowledge graphs from Wikipedia and other Wikis. The ﬁrst new dataset, CaLiGraph 1 , aims at the generation of explicit formal deﬁnitions from categories [2], and the extraction of new instances from list pages [9]. In its current release, CaLiGraph contains 200k axioms deﬁning classes, and more than 7M typed instances. In the second part, I will look at the transfer of the DBpedia approach to a multitude of arbitrary Wikis. The ﬁrst such prototype, DBkWik 2 , extracts data from Fandom, a Wiki farm hosting more than 400k different Wikis on various topics. Unlike DBpedia, which relies on a larger user base for crowdsourcing an explicit schema and extraction rules, and the “one-page-per-entity” assumption, DBkWik has to address various challenges in the ﬁelds of schema learning and data integration [3, 4]. In its current release, DBkWik contains more than 11M entities, and has been found to be highly complementary to DBpedia.
Use of a Mobile Anonymous Question-Raising System to Assist Flipped-Classroom Learning

Flipped classroom emphasizes the following. First, the instructor uses a digital platform to store course contents, including video lectures. Then, students retrieve these contents from the platform and learn by themselves before class. Finally, the instructor helps the students acquire their knowledge by asking questions in class, thereby helping the students to attain their learning goals. In previous studies, it was found that students might be affected by their peers and their own personalities, causing them not to express their opinions and views; this in turn might cause the students not to learn well; in some extreme cases, some students might even give up entirely. To solve the problem that students may hesitate to ask questions in class, this research developed a mobile anonymous question-raising system (MAQ) and used it to help students raise questions. By conducting an educational experiment, it was found that the use of MAQ in class could indeed help students to learn better in a flipped classroom setting.
Lectotypification of Some Names in Dianthus L. (Caryophyllaceae)

In this study, lectotypifications of 21 valid or synonym names of the genus Dianthus L. (Caryophyllaceae) were determined. Among these; the types of D. acrochlorus Stapf, D. haussknechtii Boiss. , D. hypochlorus Boiss. & Heldr. , D. kastembeluensis Freyn & Sint. , D. kotschyanus Boiss. & Heldr. , D. lydus Boiss. , D. micranthus Boiss. & Heldr. , D. multipunctatus Ser. var. gracilior Boiss. , D. pallens Sibth. & Sm. var. oxylepis Boiss. and D. striatellus Fenzl were based upon the specimens collected from two or more localities. The types of D. bitlisianus Kotschy ex Boiss. , D. brevicaulis Fenzl, D. carmelitarum Reut. ex Boiss. , D. cibrarius Clem. , D. hymenolepis Boiss. , D. muschianus Kotschy ex Boiss. , D. polycladus Boiss. and D. setisquameus Hausskn. ex Bornm. were based upon the specimens collected from a single locality without mentioning any “type”. And D. arpadianus Ade & Bornm. var. trojanus Bornm. & Sint. , D. engleri Hausskn. & Bornm. and D. siphonocalyx Blakelock were based upon the specimens for which multiple “types” were stated. Most of the specimens of the lectotypes determined in this study were collected from Turkey and the rest came from Syria and Iraq. Research Article