Miracle-dz/UniFAR-FTUs huggingface dataset:
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This paper describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OSX, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. SeqKit is open source and available on Github at https://github.com/shenwei356/seqkit.
European Laboratory for Particle Physics Energy Dependence of J/ψ Absorption in Proton-nucleus Collisions

Charmonium states are expected to be considerably suppressed in the case of quark-gluon plasma formation in high-energy heavy-ion collisions. However, a robust identification of suppression patterns as signatures of a deconfined QCD medium requires a detailed understanding of the " normal nuclear absorption " already present in proton-nucleus collisions, where the charmonium production cross sections increase less than linearly with the number of target nucleons. We analyse the J/ψ production cross sections measured in proton-nucleus collisions in fixed target experiments, with proton beam energies from 200 to 920 GeV, and in d-Au collisions at RHIC, at √ s NN = 200 GeV, in the framework of the Glauber formalism, using several sets of parton distributions with and without nuclear modifications. The results reveal a significant dependence of the " absorption cross section " on the kinematics of the J/ψ and on the collision energy. Extrapolating the observed patterns we derive the level of absorption expected at E lab = 158 GeV, the energy at which the heavy-ion data sets were collected at the CERN SPS.
Biomarkers in dementia: clinical utility and new directions

Imaging, cerebrospinal fluid (CSF) and blood-based biomarkers have the potential to improve the accuracy by which specific causes of dementia can be diagnosed in vivo, provide insights into the underlying pathophysiology, and may be used as inclusion criteria and outcome measures for clinical trials. While a number of imaging and CSF biomarkers are currently used for each of these purposes, this is an evolving field, with numerous potential biomarkers in varying stages of research and development. We review the currently available biomarkers for the three most common forms of neurodegenerative dementia, and give an overview of research techniques that may in due course make their way into the clinic.
Presynaptic Role of cGMP-Dependent Protein Kinase during Long-Lasting Potentiation

Previous research has suggested that cGMP-dependent protein kinases (cGKs) may play a role in long-term potentiation in hippocampus, but their site of action has been unknown. We examined this question at synapses between pairs of hippocampal neurons in dissociated cell culture. Injection of a specific peptide inhibitor of cGK into the presynaptic but not the postsynaptic neuron blocked long-lasting potentiation induced by tetanic stimulation of the presynaptic neuron. As controls, injection of a scrambled peptide or a peptide inhibitor of cAMP-dependent protein kinase into either neuron did not block potentiation. Conversely, injection of the α isozyme of cGK type I into the presynaptic but not the postsynaptic neuron produced activity-dependent potentiation that did not require NMDA receptor activation. Evidence from Western blots, reverse transcription-PCR, activity assays, and immunocytochemistry indicates that endogenous cGK type I is present in the neurons, including presynaptic terminals. These results support the idea that cGK plays an important presynaptic role during the induction of long-lasting potentiation in hippocampal neurons.
DISCOVERY OF THREE z > 6.5 QUASARS IN THE VISTA KILO-DEGREE INFRARED GALAXY (VIKING) SURVEY

Studying quasars at the highest redshifts can constrain models of galaxy and black hole formation, and it also probes the intergalactic medium in the early universe. Optical surveys have to date discovered more than 60 quasars up to z ≃ 6.4, a limit set by the use of the z-band and CCD detectors. Only one z ≳ 6.4 quasar has been discovered, namely the z = 7.08 quasar ULAS J1120+0641, using near-infrared imaging. Here we report the discovery of three new z ≳ 6.4 quasars in 332 deg2 of the Visible and Infrared Survey Telescope for Astronomy Kilo-degree Infrared Galaxy (VIKING) survey, thus extending the number from 1 to 4. The newly discovered quasars have redshifts of z = 6.60, 6.75, and 6.89. The absolute magnitudes are between −26.0 and −25.5, 0.6–1.1 mag fainter than ULAS J1120+0641. Near-infrared spectroscopy revealed the Mg ii emission line in all three objects. The quasars are powered by black holes with masses of ∼(1–2) × 109 M☉. In our probed redshift range of 6.44 < z < 7.44 we can set a lower limit on the space density of supermassive black holes of ρ(MBH > 109 M☉) > 1.1 × 10−9 Mpc−3. The discovery of three quasars in our survey area is consistent with the z = 6 quasar luminosity function when extrapolated to z ∼ 7. We do not find evidence for a steeper decline in the space density of quasars with increasing redshift from z = 6 to z = 7.
miR-Let7A Modulates Autophagy Induction in LPS-Activated Microglia

Microglia regulate the secretion of various immunomediators in central nervous system diseases. Microglial autophagy is the crucial process for cell's survival and cytokine productions. Recent studies have reported that several microRNAs are involved in the autophagy system. miR-Let7A is such a microRNA that plays a role in various inflammation responses, and is magnified as a key modulator particularly in the autophagy system. In present study, we investigated whether miR-Let7A is involved in autophagy in activating microglia. Overexpression of miR-Let7A in LPS-stimulated BV2 microglial cells promoted the induction of the autophagy related factors such as LC3II, Beclin1, and ATG3. Our results suggest a potential role of miR-Let7A in the autophagy process of microglia during CNS inflammation.
The effects of upper body exercise on the physical capacity of people with a spinal cord injury: a systematic review

Objective : To describe the effects of upper body training on the physical capacity of people with a spinal cord injury. Data sources : The databases of PubMed, CINAHL, Sport Discus and Cochrane were searched from 1970 to May 2006. Review methods : The keywords `spinal cord injury', `paraplegia', `tetraplegia' and `quadriplegia' were used in combination with `training'. The methodological quality of the included articles (both randomized controlled trials and controlled clinical trials) was assessed with the modified `van Tulder et al.' checklist. Studies were described with respect to population, test design, training protocol and mode of training. The training effects on physical capacity, reflected by peak power output (POpeak) and oxygen uptake (VO2peak), were summarized. Results : Twenty-five studies were included with a mean score of 8.8 out of 17 items on the quality checklist. The methodological quality was quite low, mostly because of the absence of randomized controlled trials. Therefore no meta-analysis was possible. In the 14 articles of acceptable quality the mean (SD) increase in VO 2peak and POpeak, following a period of training, was 17.6 (11.2)% and 26.1 (15.6)%, respectively. Conclusions : Due to the overall low quality of studies it is not possible to draw definitive conclusions on training effects for different lesion groups or training modes. The results of the relatively few studies with an acceptable quality seem to support the view that upper body exercise may increase the physical capacity of people with spinal cord injury. The magnitude of improvement in PO peak and VO2peak, however, varies considerably among studies.
Strain induced semiconductor nanotubes: from formation process to device applications

Semiconductor nanotubes (SNTs) represent a new class of nanotechnology building blocks. They are formed by a combination of bottom–up and top–down approaches, using strain induced self-rolling mechanism from epitaxially grown heterojunction films. This review summarizes several aspects of this emerging field, including the SNT formation process, its dependence on crystal orientation, strain direction and geometry as well as the structural, electronic and optical properties and their implications. The precise controllability of structural and spatial positioning and versatile functionality make SNTs and related three-dimensional (3D) architectures promising candidates for practical applications in next generation nanoelectronic and nanophotonic devices.
Evaluation of Handwriting Movement Kinematics: From an Ecological to a Magnetic Resonance Environment

Writing is a means of communication which requires complex motor, perceptual, and cognitive skills. If one of these abilities gets lost following traumatic events or due to neurological diseases, handwriting could deteriorate. Occupational therapy practitioners provide rehabilitation services for people with impaired handwriting. However, to determine the effectiveness of handwriting interventions no studies assessed whether the proposed treatments improved the kinematics of writing movement or had an effect at the level of the central nervous system. There is need to find new quantitative methodologies able to describe the behavioral and the neural outcomes of the rehabilitative interventions for handwriting. In the present study we proposed a combined approach that allowed evaluating the kinematic parameters of handwriting movements, acquired by means of a magnetic resonance-compatible tablet, and their neural correlates obtained simultaneously from a functional magnetic resonance imaging examination. Results showed that the system was reliable in term of reproducibility of the kinematic data during a test/re-test procedure. Further, despite the modifications with respect to an ecological writing movement condition, the kinematic parameters acquired inside the MR-environment were descriptive of individuals’ movement features. At last, the imaging protocol succeeded to show the activation of the cerebral regions associated with the production of writing movement in healthy people. From these findings, this methodology seems to be promising to evaluate the handwriting movement deficits and the potential alterations in the neural activity in those individuals who have handwriting difficulties. Finally, it would provide a mean to quantitatively assess the effect of a rehabilitative treatment.
Distributed Power Splitting for SWIPT in Relay Interference Channels Using Game Theory

In this paper, we consider simultaneous wireless information and power transfer (SWIPT) in relay interference channels, where multiple source-destination pairs communicate through their dedicated energy harvesting relays. Each relay needs to split its received signal from sources into two streams: one for information forwarding and the other for energy harvesting. We develop a distributed power splitting framework using game theory to derive a profile of power splitting ratios for all relays that can achieve a good network-wide performance. Specifically, non-cooperative games are respectively formulated for pure amplify-and-forward (AF) and decode-and-forward (DF) networks, in which each link is modeled as a strategic player who aims to maximize its own achievable rate. The existence and uniqueness for the Nash equilibriums (NEs) of the formulated games are analyzed and a distributed algorithm with provable convergence to achieve the NEs is also developed. Subsequently, the developed framework is extended to the more general network setting with mixed AF and DF relays. All the theoretical analyses are validated by extensive numerical results. Simulation results show that the proposed game-theoretical approach can achieve a near-optimal network-wide performance on average, especially for the scenarios with relatively low and moderate interference.
Overexpression of CDC25A phosphatase is associated with hypergrowth activity and poor prognosis of human hepatocellular carcinomas.

PURPOSE AND EXPERIMENTAL DESIGN CDC25 genes are cell cycle-activating phosphatases that positively regulate the activity of cyclin-dependent kinase. CDC25A and CDC25B, being oncogenes, are overexpressed in a variety of human malignancies. To investigate the potential roles of CDC25s in hepatocellular carcinoma (HCC), expression of CDC25A and CDC25B was examined in human HCC samples. RESULTS Reverse transcription-PCR showed that overexpression of CDC25A and CDC25B mRNAs was found in 9 of 13 (69%) and 4 of 13 (31%) HCCs, respectively. Immunohistochemistry of 59 HCCs showed marked increase in CDC25A expression, but not CDC25B, in HCC compared with noncancer tissues, and high expression of CDC25A in 33 of 59 (56%) HCCs. Overexpression of CDC25A in HCC was confirmed by Western blot analysis. High expression of CDC25A was associated with dedifferentiated phenotype and portal vein invasion (P = 0.001 and 0.031, respectively), and expression of CDC25A correlated well with proliferating cell nuclear antigen labeling index (P = 0.005). Univariate analysis indicated that high expression of CDC25A and proliferating cell nuclear antigen were both significant predictive factors for shorter disease-free survival (P = 0.004 and 0.039, respectively). Multivariate analysis indicated that CDC25A was an independent prognostic marker for disease-free survival (risk ratio for cancer relapse, 2.98; P = 0.029), even when analyzed with several clinicopathologic factors. On the other hand, expression of CDC25B did not correlate with any clinicopathological features. CONCLUSION Our findings suggest that CDC25A, but not CDC25B, could be used as an independent prognostic marker for HCC. Our data would also contribute to forward understanding of tumor biology of HCC that is associated with cell cycle regulation.
SLUG Is Expressed in Endothelial Cells Lacking Primary Cilia to Promote Cellular Calcification

Objective— Arterial calcification is considered a major cause of death and disabilities worldwide because the associated vascular remodeling leads to myocardial infarction, stroke, aneurysm, and pulmonary embolism. This process occurs via poorly understood mechanisms involving a variety of cell types, intracellular mediators, and extracellular cues within the vascular wall. An inverse correlation between endothelial primary cilia and vascular calcified areas has been described although the signaling mechanisms involved remain unknown. We aim to investigate the signaling pathways regulated by the primary cilium that modulate the contribution of endothelial cells to vascular calcification. Approach and Results— We found that human and murine endothelial cells lacking primary cilia are prone to undergo mineralization in response to bone morphogenetic proteins stimulation in vitro. Using the Tg737orpk/orpk cillium-defective mouse model, we show that nonciliated aortic endothelial cells acquire the ability to transdifferentiate into mineralizing osteogenic cells, in a bone morphogenetic protein–dependent manner. We identify &bgr;-CATENIN–induced SLUG as a key transcription factor controlling this process. Moreover, we show that the endothelial expression of SLUG is restricted to atheroprone areas in the aorta of LDLR−/− mice. Finally, we demonstrate that SLUG and phospho-homolog of the Drosophila protein, mothers against decapentaplegic (MAD) and the Caenorhabditis elegans protein SMA (from gene sma for small body size)-1/5/8 expression increases in endothelial cells constituting the vasa vasorum in the human aorta during the progression toward atherosclerosis. Conclusions— We demonstrated that the lack of primary cilia sensitizes the endothelium to undergo bone morphogenetic protein–dependent-osteogenic differentiation. These data emphasize the role of the endothelial cells on the vascular calcification and uncovers SLUG as a key target in atherosclerosis.
On the Absolutely Continuous Spectrum in a Model of an Irreversible Quantum Graph

A family Aα of differential operators depending on a real parameter α ⩾ 0 is considered. This family was suggested by Smilansky as a model of an irreversible quantum system. We find the absolutely continuous spectrum σa. c. of the operator Aα and its multiplicity for all values of the parameter. The spectrum of A0 is purely absolutely continuous and admits an explicit description. It turns out that for α<2 one has σa. c. Aα = σa. c. A0, including the multiplicity. For α⩾2 an additional branch of the absolutely continuous spectrum arises; its source is an auxiliary Jacobi matrix which is related to the operator Aα. This birth of an extra branch of the absolutely continuous spectrum is the exact mathematical expression of the effect that was interpreted by Smilansky as irreversibility. 2000 Mathematics Subject Classification 81Q10.
Cancer Stem Cells in Solid Tumors

Carcinogenesis and tumor cell biology are very complex subjects. Recent findings on cancer stem cells may have a great impact on the understanding of the biology of malignancies and the development of future treatment approaches. Cancer stem cells are defined by their potential to self-renew and differentiate. Identification of cancer stem cells is possible by detecting expression of a certain combination of various cell surface markers and also by functional assays. The cancer stem cell concept was originally developed for hematological malignancies but is now becoming accepted for solid tumors as well. Emerging data indicates that cancer stem cells are responsible for the growth and spread of tumors. There is still a long way to go in characterizing cancer stem cells and understanding their role in carcinogenesis. Further studies should lead to a greater understanding of the biology of these cells with significant implications for diagnosis, treatment, and prevention of cancer. The recent studies regarding stem cell origin of various solid tumors will be discussed briefly in this review.
Paradise Lost: The relationships between neurological and psychological changes in nicotine-dependent patients

The neural reward circuit and cognitive distortion play an important role in addiction; however, the relationship between the two has not yet been addressed. In this article, we review recent findings on nicotine dependence and propose a novel hypothesis. Previous research using functional magnetic resonance imaging (fMRI) has shown that while activation of the reward circuit (ventral striatum) appears in response to tobacco-related rewards in nicotine dependence, responses to rewards other than tobacco (e.g. food and money) are reduced. Moreover, this change is observed at the very early stages of smoking, even when a person has smoked fewer than 10 cigarettes in his/her lifetime. Thus, we propose the following hypothesis, called the Paradise Lost theory: given addicts’ lower ventral striatal responses to non-tobacco rewards, nicotine addiction disables smokers from sensing the pleasures of ordinary life (the Paradise Lost state). However, since smokers do not notice this, they produce an overestimation of tobacco (cognitive distortion), such that they do not have many pastimes other than smoking or feel that quitting smoking would reduce the happiness and pleasure and increase the difficulty of life. Cognitive distortion thus makes it difficult for smokers to take the initiative to quit smoking and even causes relapse after smoking cessation. This theory furthers our understanding of addiction and could improve our approach to the prevention and treatment of addiction.
Therapeutic effect of autologous bone marrow-derived liver stem cells transplantation in hepatitis B virus-induced liver cirrhosis.

BACKGROUND/AIMS To determine the safety, feasibility and therapeutic effect of in vitro-expanded autologous bone marrow-derived liver stem cells (BMDLSC) transplantation in cirrhotic patients following chronic hepatitis B virus infection. METHODOLOGY Twelve patients with post-hepatitic cirrhosis and portal hypertension who required splenectomy with periesophagogastric devascularization were included and were divided into two groups. Group I included six patients who received autologous BMDLSC infusion via the hepatic artery after in vitro expansion for 7 days. Group II (control group) included six patients who received normal saline infusion via the same route during splenectomy with periesophagogastric devascularization. The therapeutic effects were compared 3 months later. Patients in Group I were followed-up for 24 months after transplantation. RESULTS There were no adverse effects during short- and long-term follow-ups. Three months after the operation, patients who received BMDLSC infusion showed better hepatic function than those who received saline infusion (p<0.05). Patients in Group I showed stable liver function parameters with no complications during the 24-month follow-up period. CONCLUSIONS Transplantation of in vitro-expanded autologous BMDLSC via the hepatic artery is a safe and effective treatment for decompensated liver cirrhosis.
The incretin effect does not differ in trained and untrained, young, healthy men

After both oral and intravenous glucose administration, peripheral insulin concentrations are lower in trained compared with untrained humans. Part of this is explained by an adaptation within the β‐cell. The insulin secretion rate is higher after oral compared with intravenous glucose administration due to the release of glucagon‐like peptide‐1 (GLP‐1) and glucose‐dependent insulinotropic polypeptide (GIP) enhancing the glucose‐induced insulin secretion (the incretin effect). Our aim was to investigate whether GIP or GLP‐1 release or the incretin effect was different in trained compared with untrained humans after oral and intravenous glucose administration.
Self-calibration of the Trimble (Mensi) GS 200 terrestrial laser scanner

Terrestrial laser scanning (TLS) is a widely used technology for acquiring dense and accurate 3D information of a scene. The features and capabilities of modern TLS systems have opened the market to many new fields, such as earth science and the movie production industry. To ensure that the best quality data are captured with a TLS instrument the system needs to be free of systematic distortions. This can be accomplished through a TLS system calibration procedure by the manufacturer or through a selfcalibration procedure. This paper explores the signalized targets-based self-calibration methodology and investigates the systematic errors and precision of Trimble’s pulse-based hybrid-type laser scanner, the GS200. The instrument was calibrated twice independently in two different rooms to evaluate the stability and consistency of the systematic error parameters. Results from this research show a significant range finder offset for the given scanner and non-standard target combination. The GS200 also showed signs of systematic distortion in the vertical direction as a function of the horizontal direction, which was modelled appropriately as an empirical term. Through mathematical modelling the observed range, horizontal circle and vertical circle reading precision of the GS200 were improved in both calibrations. * Corresponding author.