Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity

Significance Although most laboratory work is performed on dividing bacteria, in the wild bacteria spend most of their lifetime in the stationary phase, scarcely dividing. To study the stationary phase, we developed a method of tracking nondividing bacteria at the single cell level and characterizing their response to external stimulation. While following bacteria under growth-arrest conditions, we found that they maintain surprisingly constant activity for several days after entering the stationary phase. These bacteria were able to produce proteins without significant cost to their viability or regrowth dynamics. Moreover, this constant-activity stationary phase enables the measurement of different bacterial characteristics, which are difficult to perform under exponential growth conditions. Exponentially growing bacteria are rarely found in the wild, as microorganisms tend to spend most of their lifetime at stationary phase. Despite this general prevalence of stationary-phase bacteria, they are as yet poorly characterized. Our goal was to quantitatively study this phase by direct observation of single bacteria as they enter into stationary phase and by monitoring their activity over several days during growth arrest. For this purpose, we devised an experimental procedure for starving single Escherichia coli bacteria in microfluidic devices and measured their activity by monitoring the production rate of fluorescent proteins. When amino acids were the sole carbon source, the production rate decreased by an order of magnitude upon entry into stationary phase. We found that, even while growth-arrested, bacteria continued to produce proteins at a surprisingly constant rate over several days. Our identification of this newly observed period of constant activity in nongrowing cells, designated as constant activity stationary phase, makes possible the conduction of assays that require constant protein expression over time, and are therefore difficult to perform under exponential growth conditions. Moreover, we show that exogenous protein expression bears no fitness cost on the regrowth of the population when starvation ends. Further characterization of constant activity stationary phase—a phase where nongrowing bacteria can be quantitatively studied over several days in a reproducible manner—should contribute to a better understanding of this ubiquitous but overlooked physiological state of bacteria in nature.
Recovering sound sources from embedded repetition

Cocktail parties and other natural auditory environments present organisms with mixtures of sounds. Segregating individual sound sources is thought to require prior knowledge of source properties, yet these presumably cannot be learned unless the sources are segregated first. Here we show that the auditory system can bootstrap its way around this problem by identifying sound sources as repeating patterns embedded in the acoustic input. Due to the presence of competing sounds, source repetition is not explicit in the input to the ear, but it produces temporal regularities that listeners detect and use for segregation. We used a simple generative model to synthesize novel sounds with naturalistic properties. We found that such sounds could be segregated and identified if they occurred more than once across different mixtures, even when the same sounds were impossible to segregate in single mixtures. Sensitivity to the repetition of sound sources can permit their recovery in the absence of other segregation cues or prior knowledge of sounds, and could help solve the cocktail party problem.
An Ageing Methadone Population: A Challenge to Aged Persons’ Mental Health Services?

Oral administration of methadone has been used as a treatment strategy for opiate addiction for many years. The state of Victoria, Australia, has a long-running methadone program with a large number of participants. Accordingly, a growing number of adults have utilised methadone maintenance treatment for a number of years and are now moving into older age due to advances in medical treatment and harm reduction initiatives. The objective of this review is to examine the literature pertaining to co-occurring mental illness in older methadone treatment participants and to explore the future challenges this growing cohort of ageing adults pose to aged persons’ psychiatry services. As part of a broader study into dual diagnosis in older adults, a search of the Scopus, ProQuest, and CINAHL journal databases was performed. Twenty abstracts from literature published within the previous 15 years (1999–2014) were identified that explored methadone maintenance programs and the older adults maintained on them. A number of researchers have identified the ageing methadone population to have a high degree of comorbid mental illness and psychological distress. Studies also indicate that individuals enrolled in methadone maintenance programs may engage in a degree of continual substance use, potentially leading to deleterious effects on their psychosocial function. An ageing methadone population experiencing a high degree of comorbid mental illness is likely to challenge aged persons’ psychiatry services. These services are likely to be increasingly called on to manage these individuals, particularly within Victoria where few substance use services exist for those over the age of 65. It is essential that aged persons’ psychiatry services prepare to provide care for these individuals in a responsive manner that is inclusive of both their mental health and substitution pharmacotherapy.
Effects of a Single Bout of Interval Hypoxia on Cardiorespiratory Control and Blood Glucose in Patients With Type 2 Diabetes

OBJECTIVE Hypoxia may cause functional autonomic imbalance in diabetes. Intermittent hypoxia (IH), a technique improving the adaptation to hypoxia, might improve cardiorespiratory reflexes and, ultimately, blood glucose concentrations in patients with type 2 diabetes. We tested whether a single bout of IH could initiate a long-lasting response potentially leading to better adaptation to hypoxia. RESEARCH DESIGN AND METHODS In 14 patients with type 2 diabetes without autonomic complications, we measured blood pressure, heart rate, oxygen saturation, chemoreflex (hypoxic and hypercapnic ventilatory responses, ventilatory recruitment threshold), and baroreflex sensitivity before, immediately after, and 3 and 6 h after a 1-h single bout of IH (6-min breathing of 13% oxygen mixture 5 times each separated by 6-min recovery). The measurements were repeated on a placebo day (at least 1 week apart, in random sequence) when subjects were only breathing room air (single-blind protocol). RESULTS IH significantly increased hypercapnic ventilatory responses and reduced ventilatory recruitment threshold, and increased oxygen saturation and blood pressures, whereas increases in heart rate variability and baroreflex sensitivity were not significant. Blood glucose significantly decreased after IH. No such changes were observed during the placebo day, except an increase in oxygen saturation. Some of the effects lasted 3 h after IH, and some even persisted until 6 h after IH. CONCLUSIONS A single bout of IH induced an initial adaptation to hypoxia, with improvement in cardiorespiratory reflexes and reduction in blood glucose. Patients with type 2 diabetes could potentially benefit from the application of a full (>2 weeks) IH intervention.
Soluble fms-like tyrosine kinase-1 (sFLT-1) predicts post-percutaneous coronary intervention (PCI) myocardial infarction (MI type 4a)

Context: Acute myocardial infarction (AMI) related to percutaneous coronary intervention (PCI) (MI type 4a) occurs in up to 26% of elective patients. Objective: To evaluate if sFLT-1 helps to predict MI type 4a in troponin negative patients with elective PCI. Materials and methods: We enrolled 135 patients, 106 had a PCI. sFLT-1 levels were assessed at five time points before and after PCI. Results: MI type 4a occurred in 22.1% of patients. sFLT-1 levels at admission above 251 pg/mL indicated a significant relative risk for MI type 4a of 2.83. Conclusion and discussion: Increased sFLT-1 levels at baseline might indicate unstable atherosclerosis and risk for microembolization and thus be predictive of MI type 4a.
Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum

Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.
The G209A mutation in the alpha-synuclein gene is not detected in familial cases of Parkinson disease in non-Greek and/or Italian populations.

OBJECTIVE To determine whether the G-to-A substitution at nucleotide 209 (G209A) mutation in the alpha-synuclein gene is responsible for familial Parkinson disease (PD) in the US population. DESIGN Polymerase chain reaction-based DNA analysis of consecutive patients with PD and family history of PD. SETTING A university-affiliated movement disorder clinic and a Veterans Affairs clinical research laboratory. PATIENTS Forty-four patients with PD and family history of PD and 29 patients with sporadic PD, all with no known Greek and/or Italian background. RESULTS None of the DNA samples showed the G209A mutation. CONCLUSION The G209A mutation is rare in US patients with familial PD.
An Acoustic Comparison of Vowel Length Contrasts in Standard Arabic, Japanese and Thai

In our earlier perception study, we observed that familiarity with first language (L1) phonemic length contrasts in Japanese does not transfer optimally into an unknown language, Arabic. We hypothesized that this finding is related to cross-language differences in how vowel length contrasts are phonetically realized. The present study compares vowel length contrasts that are phonemic in three typologically unrelated languages, i.e., Standard Arabic, Japanese and Thai, in an attempt to understand the extent to which vowel length contrasts are similar or dissimilar in these languages. Acoustic measurements showed short and long categories were clearly differentiated in all three languages and the short-to-long ratio did not substantially differ across languages. This suggests that listeners attend to more than just acoustic vowel duration in making perceptual judgments on short vs. long vowels.
A Systematic Comparison of the Properties of Clinically Used Angiotensin II Type 1 Receptor Antagonists

Angiotensin II type 1 receptor antagonists (ARBs) have become an important drug class in the treatment of hypertension and heart failure and the protection from diabetic nephropathy. Eight ARBs are clinically available [azilsartan, candesartan, eprosartan, irbesartan, losartan, olmesartan, telmisartan, valsartan]. Azilsartan (in some countries), candesartan, and olmesartan are orally administered as prodrugs, whereas the blocking action of some is mediated through active metabolites. On the basis of their chemical structures, ARBs use different binding pockets in the receptor, which are associated with differences in dissociation times and, in most cases, apparently insurmountable antagonism. The physicochemical differences between ARBs also manifest in different tissue penetration, including passage through the blood-brain barrier. Differences in binding mode and tissue penetration are also associated with differences in pharmacokinetic profile, particularly duration of action. Although generally highly specific for angiotensin II type 1 receptors, some ARBs, particularly telmisartan, are partial agonists at peroxisome proliferator-activated receptor-γ. All of these properties are comprehensively reviewed in this article. Although there is general consensus that a continuous receptor blockade over a 24-hour period is desirable, the clinical relevance of other pharmacological differences between individual ARBs remains to be assessed.
Automated respiratory cycles selection is highly specific and improves respiratory mechanics analysis

Objective: Selected optimal respiratory cycles should allow calculation of respiratory mechanic parameters focusing on patient–ventilator interaction. New computer software automatically selecting optimal breaths and respiratory mechanics derived from those cycles are evaluated. Design: Retrospective study. Setting: University level III neonatal intensive care unit. Subjects: Ten mins synchronized intermittent mandatory ventilation and assist/control ventilation recordings from ten newborns. Intervention: The ventilator provided respiratory mechanic data (ventilator respiratory cycles) every 10 secs. Pressure, flow, and volume waves and pressure-volume, pressure-flow, and volume-flow loops were reconstructed from continuous pressure-volume recordings. Visual assessment determined assisted leak-free optimal respiratory cycles (selected respiratory cycles). New software graded the quality of cycles (automated respiratory cycles). Respiratory mechanic values were derived from both sets of optimal cycles. We evaluated quality selection and compared mean values and their variability according to ventilatory mode and respiratory mechanic provenance. To assess discriminating power, all 45 “t” values obtained from interpatient comparisons were compared for each respiratory mechanic parameter. Measurements and Main Results: A total of 11,724 breaths are evaluated. Automated respiratory cycle/selected respiratory cycle selections agreement is high: 88% of maximal &kgr; with linear weighting. Specificity and positive predictive values are 0.98 and 0.96, respectively. Averaged values are similar between automated respiratory cycle and ventilator respiratory cycle. C20/C alone is markedly decreased in automated respiratory cycle (1.27 ± 0.37 vs. 1.81 ± 0.67). Tidal volume apparent similarity disappears in assist/control: automated respiratory cycle tidal volume (4.8 ± 1.0 mL/kg) is significantly lower than for ventilator respiratory cycle (5.6 ±1.8 mL/kg). Coefficients of variation decrease for all automated respiratory cycle parameters in all infants. “t” values from ventilator respiratory cycle data are two to three times higher than ventilator respiratory cycles. Conclusions: Automated selection is highly specific. Automated respiratory cycle reflects most the interaction of both ventilator and patient. Improving discriminating power of ventilator monitoring will likely help in assessing disease status and following trends. Averaged parameters derived from automated respiratory cycles are more precise and could be displayed by ventilators to improve real-time fine tuning of ventilator settings.
Empirical analysis of power management schemes for multi-core smartphones

Dynamic power management schemes in mobile devices such as smartphones and tablet PCs enhance battery life at the cost of prolonged user-perceived response time while the response time is a crucial factor for user experience. This paper presents systematic analysis of existing power management schemes adopted in recent smartphones in terms of user-perceived response time and energy consumption. For this analysis, we developed a latency measurement benchmark tool to quantify responsiveness to user inputs and used it with an externally-connected power meter to concurrently measure energy consumption and response latency. The evaluation showed that some existing DVFS schemes can significantly harm the response time. More seriously, the analysis revealed that the processor hotplug technique for multi-core systems may reduce responsiveness even without any gain in energy savings.
Sentiment Classification with Convolutional Neural Networks: An Experimental Study on a Large-Scale Chinese Conversation Corpus

Previous research on sentiment classification by machine learning algorithms has shown that they usually work well with large-scale dataset. However, most open datasets for Chinese sentiment classification are quite small. In this paper we build a large-scale annotated Chinese sentiment dataset by filtering a vast amount of human-computer conversations. We conduct thorough experiments by using Convolutional Neural Networks (CNNs) and other classical machine learning methods. The experimental evaluation is made on a human-annotated dataset and COAE2014 task. The extensive experiments demonstrate that Chinese sentiment classification task can benefit from our dataset and CNNs model can achieve better performance than classical machine learning approaches.
Pulsed Color-Flow Doppler Analysis of Arterial Deficiency in Idiopathic Clubfoot

This prospective study used pulsed color-flow Doppler sonography to determine differences in the presence and direction of flow through the dorsalis pedis, posterior tibial, and peroneal arteries in a group of children with clubfoot and a comparison group of controls. There was a statistically significant difference in the prevalence of deficient (absent or retrograde flow) dorsalis pedis arteries in children with clubfoot (45%) compared with controls (8%). This indicates that there is an association between some clubfeet and deficiency of the dorsalis pedis artery. There was a trend toward difference in the prevalence of deficiency of the dorsalis pedis artery in the clubfeet that required surgery (54%) compared with those that did not (20%), suggesting that dorsalis pedis artery deficiency may be more prevalent among clubfeet with greater deformity.
Effect of Substrate Depth and Planting Season on Sedum Plug Survival on Green Roofs

Abstract Green roofs, a roofing technology that entails growing plants on rooftops, provide many benefits such as improved stormwater management, energy conservation, mitigation of the urban heat island effect, increased longevity of roofing membranes, reduction in noise and air pollution, and improved aesthetics. Plants on rooftops are more susceptible to extremes in temperature and drought due to their shallow substrate and elevation above ground. Because of these unfavorable growing conditions, plant selection and season of establishment are critical. The major objective of this study was to quantify the effect of substrate depth and planting season on successful establishment of plugs of Sedum species on green roofs. Plugs of nine species of Sedum were planted in East Lansing, MI, in autumn (September 20, 2004) or spring (June 8, 2005) and then evaluated for survival on June 1, 2005, and June 1, 2006, respectively. Overall, spring planting exhibited superior survival rates (81%) compared to autumn (23.
Finding Co-Clusters of Genes and Clinical Parameters

For better understanding of genetic mechanisms underlying clinical observations, we often want to determine which genes and clinical traits are interrelated. We introduce a computational method that can find co-clusters or groups of genes and clinical parameters that are believed to be closely related to each other based upon given empirical information. The proposed method was tested with data from an acute myelogenous leukemia (AML) study and identified statistically significant co-clusters of genes and clinical traits. The validation of our results with gene ontology (GO) as well as the literature suggest that the proposed method can provide biologically meaningful co-clusters of genes and traits
The Autographa californica Multicapsid Nucleopolyhedrovirus GP64 Protein: Analysis of Transmembrane Domain Length and Sequence Requirements

ABSTRACT GP64, the major envelope glycoprotein of the Autographa californica multicapsid nucleopolyhedrovirus budded virion, is important for host cell receptor binding and mediates low-pH-triggered membrane fusion during entry by endocytosis. Previous transmembrane (TM) domain replacement studies showed that the TM domain serves a critical role in GP64 function. To extend the prior studies and examine specific sequence requirements of the TM domain, we generated a variety of GP64 TM domain mutations. The mutations included 4- to 8-amino-acid deletions, as well as single and multiple point mutations. While most TM domain deletion constructs remained fusion competent, those containing deletions of eight amino acids from the C terminus did not mediate detectable fusion. The addition of a hydrophobic amino acid (A, L, or V) to the C terminus of construct C8 (a construct that contains a TM domain deletion of eight amino acids from the C terminus) restored fusion activity. These data suggest that the membrane fusion function of GP64 is dependent on a critical length of the hydrophobic TM domain. All GP64 proteins with a truncated TM domain mediated detectable virion budding with dramatically lower levels of efficiency than wild-type GP64. The effects of deletions of various lengths and positions in the TM domain were also examined for their effects on viral infectivity. Further analysis of the TM domain by single amino acid substitutions and 3-alanine scanning mutations identified important but not essential amino acid positions. These studies showed that amino acids at positions 485 to 487 and 503 to 505 are important for cell surface expression of GP64, while amino acids at positions 483 to 484 and 494 to 496 are important for virus budding. Overall, our results show that specific features and amino acid sequences, particularly the length of the hydrophobic TM domain, play critical roles in membrane anchoring, membrane fusion, virus budding, and infectivity.
Analysis of Chemokine Receptor Gene Expression in Esophageal Cancer Cells Compared with Breast Cancer with Insights into Metastasis

Background: Chemokine receptors have been shown to play an important role in the development and metastatic spread of various malignancies. In this study, the gene expression profile of some key chemokine receptors involved in metastasis has been investigated in esophageal and breast cancer cell lines. Methods: In a descriptive study, gene expression profile of CCR1, CCR6, CCR7, CCR9, CXCR1, and CXCR4 in human esophageal cancer cell line (KYSE-30) and human breast cancer cell line (MCF7) were analyzed using real-time PCR and their results were compared accordingly. Results: We demonstrated for the first time the expression of CCR1, CCR6, CCR7, CCR9, CXCR1, and CXCR4 at transcriptional level in human esophageal cancer cell line. The expression of CCR1, CCR7 and CXCR4 were lower in esophageal compared with breast cancer cells, although without significant difference. CCR9 was highly expressed in esophageal cancer cells as compared to the breast cancer cells (P < 0.05). Similarly, the expression of CCR6 and CXCR1 were higher, although without significant difference. Conclusion: Esophageal cancer cells like breast cancer express some key chemokine receptors involved in metastasis. Targeting of proposed receptors in esophageal cancer may be a novel strategy for prevention of cancer metastasis.