Miracle-dz/UniFAR-FTUs huggingface dataset:
Polynomial Loops: Beyond Termination

In the last years, several works were concerned with identifying classes of programs where termination is decidable. We consider triangular weakly non-linear loops ( twn -loops) over a ring Z ≤ S ≤ R A , where R A is the set of all real algebraic numbers. Essentially, the body of such a loop is a single assignment (cid:16) x 1 . x d (cid:17) ← (cid:16) c 1 · x 1 + pol 1 . c d · x d + pol d (cid:17) where each x i is a variable, c i ∈ S , and each pol i is a (possibly non-linear) polynomial over S and the variables x i +1 , . , x d . Recently, we showed that termination of such loops is decidable for S = R A and non-termination is semi-decidable for S = Z and S = Q [19]. In this paper, we show that the halting problem is decidable for twn -loops over any ring Z ≤ S ≤ R A . In contrast to the termination problem, where termination on all inputs is considered, the halting problem is concerned with termination on a given input. This allows us to compute witnesses for non-termination . Moreover, we present the ﬁrst computability results on the runtime complexity of such loops. More precisely, we show that for twn -loops over Z one can always compute a polynomial f such that the length of all terminating runs is bounded by f ( (cid:107) ( x 1 , . . . , x d ) (cid:107) ), where (cid:107) · (cid:107) denotes the 1-norm. As a corollary, we obtain that the runtime of a terminating triangular linear loop over Z
Feasibility, acceptability and affective consequences of at‐home sleep extension in young women with depressive symptoms: A pilot study

Insufficient sleep is common in young adults and has meaningful consequences for daytime functioning, including increased sleepiness, affective disruption and depressive symptoms. This study provides a preliminary evaluation of the feasibility, acceptability and affective consequences of extended sleep opportunity in young women with insufficient sleep and depressive symptoms. Participants were 32 women, 18–22 years of age, who regularly obtained less than 8‐hr sleep/night and had daytime sleepiness and depressive symptoms at or above population averages. Participants were asked to maintain a sleep schedule of their typical duration for 7 days and were then randomly assigned to either extend sleep opportunity (ESO) by 90 min per night or maintain typical sleep opportunity (TSO), for the next 7 days. Sleep characteristics and daytime sleepiness were measured using continuous actigraphy and daily sleep diary, and affect, stress and depressive symptoms were assessed with daily and weekly questionnaires. Extended sleep opportunity increased sleep duration by over 1 hr, improved morning sleepiness and positive affect, and diminished anhedonia and depressive symptoms in study completers (n = 11 ESO, 11 TSO). However, 31.3% of participants (n = 10) were withdrawn from the study due to difficulty maintaining the sleep schedule. These results provide initial evidence that sleep extension is beneficial for young women who usually have inadequate sleep and mood disruption and can maintain a consistent sleep schedule. If extending sleep opportunity improves sleep, daytime sleepiness and affect in young adults who typically have insufficient sleep, it could broaden the range of interventions for sleep and mental wellness.
Canonical Notch signaling controls the early thymic epithelial progenitor cell state and emergence of the medullary epithelial lineage in fetal thymus development

ABSTRACT Thymus function depends on the epithelial compartment of the thymic stroma. Cortical thymic epithelial cells (cTECs) regulate T cell lineage commitment and positive selection, while medullary (m) TECs impose central tolerance on the T cell repertoire. During thymus organogenesis, these functionally distinct sub-lineages are thought to arise from a common thymic epithelial progenitor cell (TEPC). However, the mechanisms controlling cTEC and mTEC production from the common TEPC are not understood. Here, we show that emergence of the earliest mTEC lineage-restricted progenitors requires active NOTCH signaling in progenitor TEC and that, once specified, further mTEC development is NOTCH independent. In addition, we demonstrate that persistent NOTCH activity favors maintenance of undifferentiated TEPCs at the expense of cTEC differentiation. Finally, we uncover a cross-regulatory relationship between NOTCH and FOXN1, a master regulator of TEC differentiation. These data establish NOTCH as a potent regulator of TEPC and mTEC fate during fetal thymus development, and are thus of high relevance to strategies aimed at generating/regenerating functional thymic tissue in vitro and in vivo. Summary: Notch signaling regulates the initial emergence of medullary thymic epithelial sublineage, implicating Notch in the maintenance of primitive thymic epithelial progenitors and uncovering its cross-interaction with Foxn1.
Host cytosolic RNA sensing pathway promotes T Lymphocyte-mediated mycobacterial killing in macrophages

Mycobacterial infection leads to activation of the RIG-I/MAVS/TBK1 RNA sensing pathway in macrophages but the consequences of this activation remains poorly defined. In this study, we determined that activation of this RNA sensing pathway stimulates ICAM-1 expression in M.avium-infected macrophage through the inhibition of the E3 ubiquitin ligase CRL4COP1/DET1. CRL4 when active targets the transcription factor ETV5 for degradation by the ubiquitin–proteasome system. In the absence of the ETV5 transcription factor, ICAM-1 expression is significantly decreased. The M.avium-induced ICAM-1 production is required for the formation of immune synapse between infected macrophages and antigen-specific CD4+ T lymphocytes, and is essential for CD4+ T lymphocyte-mediated mycobacterial killing in vitro and in mice. This study demonstrates a previously undefined mechanism by which a host cytosolic RNA sensing pathway contributes to the interplay between mycobacteria infected macrophages and antigen-specific T lymphocytes.
Effect of AGER on the biological behavior of non-small cell lung cancer H1299 cells

Advanced glycosylation end-product specific receptor (AGER) is a multi-ligand cell surface receptor abnormally expressed in lung cancer, and is a member of the immunoglobulin superfamily. Therefore, this study aimed to explore the effect of AGER on the biological behavior of non-small cell lung cancer (NSCLC) H1299 cell line. A microarray-based gene expression profiling analysis of the GSE27262 dataset from the Gene Expression Omnibus (GEO) database was conducted to identify differentially expressed genes, which were verified using The Cancer Genome Atlas (TCGA) database. The expression of AGER in the normal human lung BEAS-2B cell line and NSCLC H1299 cell line was examined using reverse transcription-quantitative PCR. Lentiviral interference and overexpression vectors of AGER were constructed and transfected into H1299 cells using Lipofectamine®. AGER expression and biological properties, including cell viability, apoptosis, migration and invasion abilities, in H1299 cells were investigated using MTT, flow cytometry, wound healing and Transwell assays. AGER was expressed at a low level in NSCLC tissues and H1299 cells (P<0.05). Compared with control cells, AGER overexpression cells displayed decreased cell viability, proliferation, migration and invasion abilities, and significantly increased levels of apoptosis. Furthermore, AGER overexpression increased the expression of Bax and decreased the expression of Bcl-2 in H1299 cells (P<0.05), and AGER knockdown displayed the opposite effects on H1299 cells. Therefore, AGER overexpression decreased the proliferation, invasion and migration abilities of H1299 cells, and increased apoptosis. The present study suggested that AGER might serve as a potential molecular marker for NSCLC.
Structural Elucidation of Antibiotic TKR2999, an Antifungal Lipodepsipeptide Isolated from the Fungus Foliophoma fallens

An antifungal lipodepsipeptide was obtained from cultures of the fungus Foliophoma fallens CF-236885. Its structure, elucidated by HRMS and NMR spectroscopy, contained Gly, Thr, Asn, β-Ala, Orn, Ala, two Ser residues, and 3-hydroxy-4-methylhexadecanoic acid. The absolute configuration of its amino acid residues was determined using Marfey’s analysis and J-based configuration analysis helped to establish the relative configuration of the 3-hydroxy-4-methylhexadecanoic acid moiety. A literature search retrieved a patent describing antibiotic TKR2999 (1), whose non-disclosed structure was confirmed to be identical to that found for our compound, according to its physicochemical properties and NMR spectra. Compound 1 displayed potent antifungal activity against Aspergillus fumigatus and a panel of Candida strains.
The Structural, Electronic, and Optical Properties of Ge/Si Quantum Wells: Lasing at a Wavelength of 1550 nm

The realization of a fully integrated group IV electrically driven laser at room temperature is an essential issue to be solved. We introduced a novel group IV side-emitting laser at a wavelength of 1550 nm based on a 3-layer Ge/Si quantum well (QW). By designing this scheme, we showed that the structural, electronic, and optical properties are excited for lasing at 1550 nm. The preliminary results show that the device can produce a good light spot shape convenient for direct coupling with the waveguide and single-mode light emission. The laser luminous power can reach up to 2.32 mW at a wavelength of 1550 nm with a 300-mA current. Moreover, at room temperature (300 K), the laser can maintain maximum light power and an ideal wavelength (1550 nm). Thus, this study provides a novel approach to reliable, efficient electrically pumped silicon-based lasers.
Dissecting the Genetic Architecture of Cystatin C in Diversity Outbred Mice

Plasma concentration of Cystatin C (CysC) level is a biomarker of glomerular filtration rate in the kidney. We use a Systems Genetics approach to investigate the genetic determinants of plasma CysC concentration. To do so we perform Quantitative Trait Loci (QTL) and expression QTL (eQTL) analysis of 120 Diversity Outbred (DO) female mice, 56 weeks of age. We performed network analysis of kidney gene expression to determine if the gene modules with common functions are associated with kidney biomarkers of chronic kidney diseases. Our data demonstrates that plasma concentrations and kidney mRNA levels of CysC are associated with genetic variation and are transcriptionally coregulated by immune genes. Specifically, Type-I interferon signaling genes are coexpressed with Cst3 mRNA levels and associated with CysC concentrations in plasma. Our findings demonstrate the complex control of CysC by genetic polymorphisms and inflammatory pathways.
AFLP-SSR maps of maize×teosinte and maize×maize : Comparison of map length and segregation distortion

Two genetic linkage maps of Zea mays were constructed: one population comprised 94 F 2 individuals of a dent 'B64' x teosinte (Z. mays ssp. huehuetenangensis) cross while the second consisted of 94 F 2 individuals of a 'B64' x Caribbean flint 'Na4' cross. The level of polymorphism was higher in the 'B64' x teosinte combination than the 'B64' x 'Na4' combination. In the 'B64' x teosinte cross, a total of 338 amplified fragment length polymorphism (AFLP) and 75 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 1402.4 cM. In the 'B64' x 'Na4' cross, a total of 340 AFLP and 97 SSR markers were mapped to 10 chromosomes, covering 1662.8 cM. Segregation distortion regions were found on chromosomes 4, 5 and 8 in the 'B64' x teosinte cross and on chromosome 9 in the 'B64' x 'Na4' cross. Comparison of the two maps revealed that the maize x teosinte map was 11.5% shorter than the maize x maize map. The maps generated in this study may be useful to identify genes controlling flooding tolerance.
Paramedics’ Perspectives on the Hospital Transfers of Nursing Home Residents—A Qualitative Focus Group Study

Emergency department (ED) visits and hospital admissions are common among nursing home residents (NHRs). Little is known about the perspectives of emergency medical services (EMS) which are responsible for hospital transports. The aim of this study was to explore paramedics’ experiences with transfers from nursing homes (NHs) and their ideas for possible interventions that can reduce transfers. We conducted three focus groups following a semi-structured question guide. The data were analyzed by content analysis using the software MAXQDA. In total, 18 paramedics (mean age: 33 years, male n = 14) participated in the study. Paramedics are faced with complex issues when transporting NHRs to hospital. They mainly reported on structural reasons (e.g., understaffing or lacking availability of physicians), which led to the initiation of an emergency call. Handovers were perceived as poorly organized because required transfer information (e.g., medication lists, advance directives (ADs)) were incomplete or nursing staff was insufficiently prepared. Hospital transfers were considered as (potentially) avoidable in case of urinary catheter complications, exsiccosis/infections and falls. Legal uncertainties among all involved professional groups (nurses, physicians, dispatchers, and paramedics) seemed to be a relevant trigger for hospital transfers. In paramedics’ point of view, emergency standards in NHs, trainings for nursing staff, the improvement of working conditions and legal conditions can reduce potentially avoidable hospital transfers from NHs.
Selfishness in Vehicular Delay-Tolerant Networks: A Review

Various operational communication models are using Delay-Tolerant Network as a communication tool in recent times. In such a communication paradigm, sometimes there are disconnections and interferences as well as high delays like vehicle Ad hoc networks (VANETs). A new research mechanism, namely, the vehicle Delay-tolerant network (VDTN), is introduced due to several similar characteristics. The store-carry-forward mechanism in VDTNs is beneficial in forwarding the messages to the destination without end-to-end connectivity. To accomplish this task, the cooperation of nodes is needed to forward messages to the destination. However, we cannot be sure that all the nodes in the network will cooperate and contribute their computing resources for message forwarding without any reward. Furthermore, there are some selfish nodes in the network which may not cooperate to forward the messages, and are inclined to increase their own resources. This is one of the major challenges in VDTNs and incentive mechanisms are used as a major solution. This paper presents a detailed study of the recently proposed incentive schemes for VDTNs. This paper also gives some open challenges and future directions for interested researchers in the future.
Complete Genome Sequences of Five Salmonella enterica Phages, NBSal001, NBSal002, NBSal003, NBSal004, and NBSal005

Salmonella enterica is a Gram-negative bacterium, recognized as one of the most important foodborne pathogens in the world. Bacteriophages represent a promising alternative to the biocontrol of Salmonella. Here, we report the isolation of five Salmonella bacteriophages, the sequencing of their full genomes, and initial genomic characterization. ABSTRACT Salmonella enterica is a Gram-negative bacterium, recognized as one of the most important foodborne pathogens in the world. Bacteriophages represent a promising alternative to the biocontrol of Salmonella. Here, we report the isolation of five Salmonella bacteriophages, the sequencing of their full genomes, and initial genomic characterization.
Identification of Genes Potentially Involved in Pearl Formation by Expressed Sequence Tag Analysis of Mantle from Freshwater Pearl Mussel (Hyriopsis Cumingii Lea)

ABSTRACT The triangle sail mussel (Hyriopsis cumingii Lea) is the most important mussel species exploited for commercial freshwater pearl production in China. However, little is known about the genes that arc involved in pearl formation. A complementary DNA library from mantle tissue of Hyriopsis cumingii was constructed to identify the genes required for pearl formation. A total of 5,019 expressed sequence tags (ESTs) were sequenced, which resulted in the identification of 620 contigs and 1,151 singletons. BLAST analysis showed that nearly half (44.7%) of these unigenes were homologous to the known genes and 55.3% were genes with unknown functions. Based on the sequence similarities, 29 genes were putatively involved in pearl formation. These EST data provide the basis for future studies of the molecular mechanisms underlying pearl formation.
Urinary 8-OHdG as a Biomarker for Oxidative Stress: A Systematic Literature Review and Meta-Analysis

Oxidative stress reflects a disturbance in the balance between the production and accumulation of reactive oxygen species (ROS). ROS are scavenged by the antioxidant system, but when in excess concentration, they can oxidize proteins, lipids, and DNA. DNA damage is usually repaired, and the oxidized products are excreted in urine. 8-hydroxy-2-deoxyguanosine is considered a biomarker for oxidative damage of DNA. It is needed to define background ranges for 8-OHdG, to use it as a measure of oxidative stress overproduction. We established a standardized protocol for a systematic review and meta-analysis to assess background ranges for urinary 8-OHdG concentrations in healthy populations. We computed geometric mean (GM) and geometric standard deviations (GSD) as the basis for the meta-analysis. We retrieved an initial 1246 articles, included 84 articles, and identified 128 study subgroups. We stratified the subgroups by body mass index, gender, and smoking status reported. The pooled GM value for urinary 8-OHdG concentrations in healthy adults with a mean body mass index (BMI) ≤ 25 measured using chemical methods was 3.9 ng/mg creatinine (interquartile range (IQR): 3 to 5.5 ng/mg creatinine). A significant positive association was observed between smoking and urinary 8-OHdG concentrations when measured by chemical analysis. No gender effect was observed.
Syncope, "Mechanical Falls," and the Trauma Surgeon.

I n 2016, 44% of trauma patients included in the American College of Surgeons' National Trauma Data Bank had suffered falls, accounting for more trauma admissions than the next four most common mechanisms combined. The prevalence of falls has been on an upward trajectory for over a decade, and falls are more prevalent than all other injury mechanisms combined in patients over the age of 55 years. It is no coincidence that the percentage of falls has increased as the percentage of elderly patients (age 65 years or older) has risen (Fig. 1). The energy transfer after a fall is directly related to the height of the fall. However, serious injuries can occur even after ground level falls, particularly in the elderly. This is related in part to the manner in which the patient falls, decreased bone density, and the use of antithrombotic medications. Once injured, for essentially every type of injury that has been studied, elderly trauma patients suffer worse outcomes compared with younger patients with similar injury severity. Outcomes are impacted by physiology, frailty, and comorbid medical conditions. The same factors that relate to poor outcomes can also contribute to falls. Consequently, when we encounter an older fall victim, the reason for the fall is relevant. We must identify and manage the injuries and at the same time determine whether there is a treatable condition associated with the fall itself. Recognizing that a syncopal event could be a sign of an underlying life-threatening condition, it is critical to identify it as such and do a proper evaluation. However, what does that entail? There is great variability in what is performed as a syncope workup (unpublished data, Southwestern Surgical Congress [SWSC] Multicenter Trial abstract 2020), and in this document we will offer an evidence-based algorithm. However, it is also important to recognize that a nonsyncopal fall may also be a sign of a significant medical condition or an indication that there are causative factors that warrant intervention.
A Comparison of Different Counting Methods for a Holographic Particle Counter: Designs, Validations and Results

Digital Inline Holography (DIH) is used in many fields of Three-Dimensional (3D) imaging to locate micro or nano-particles in a volume and determine their size, shape or trajectories. A variety of different wavefront reconstruction approaches have been developed for 3D profiling and tracking to study particles’ morphology or visualize flow fields. The novel application of Holographic Particle Counters (HPCs) requires observing particle densities in a given sampling volume which does not strictly necessitate the reconstruction of particles. Such typically spherical objects yield circular intereference patterns—also referred to as fringe patterns—at the hologram plane which can be detected by simpler Two-Dimensional (2D) image processing means. The determination of particle number concentrations (number of particles/unit volume [#/cm3]) may therefore be based on the counting of fringe patterns at the hologram plane. In this work, we explain the nature of fringe patterns and extract the most relevant features provided at the hologram plane. The features aid the identification and selection of suitable pattern recognition techniques and its parameterization. We then present three different techniques which are customized for the detection and counting of fringe patterns and compare them in terms of detection performance and computational speed.
Draft Genome Sequences of Nine Cultivable Heterotrophic Proteobacteria Isolated from Phycosphere Microbiota of Toxic Alexandrium catenella LZT09

Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean. ABSTRACT Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean.