Miracle-dz/UniFAR-FTUs huggingface dataset:
Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

Metabolic diversity in microorganisms can provide the basis for creating novel biochemical products. However, most metabolic engineering projects utilize a handful of established model organisms and thus, a challenge for harnessing the potential of novel microbial functions is the ability to either heterologously express novel genes or directly utilize non-model organisms. Genetic manipulation of non-model microorganisms is still challenging due to organism-specific nuances that hinder universal molecular genetic tools and translatable knowledge of intracellular biochemical pathways and regulatory mechanisms. However, in the past several years, unprecedented progress has been made in synthetic biology, molecular genetics tools development, applications of omics data techniques, and computational tools that can aid in developing non-model hosts in a systematic manner. In this review, we focus on concerns and approaches related to working with non-model microorganisms including developing molecular genetics tools such as shuttle vectors, selectable markers, and expression systems. In addition, we will discuss: (1) current techniques in controlling gene expression (transcriptional/translational level), (2) advances in site-specific genome engineering tools [homologous recombination (HR) and clustered regularly interspaced short palindromic repeats (CRISPR)], and (3) advances in genome-scale metabolic models (GSMMs) in guiding design of non-model species. Application of these principles to metabolic engineering strategies for consolidated bioprocessing (CBP) will be discussed along with some brief comments on foreseeable future prospects.
Trans‐substitution of the proximal hydrogen bond in myoglobin: I. Structural consequences of hydrogen bond deletion

The structural role of a side‐chain to side‐chain protein hydrogen bond is examined using trans‐substitution of the proximal histidine of myoglobin with methylimidazoles (Barrick, Biochemistry 1994 ;33:6546–6554). Modification of the chemical structure of exogenous ligands allows this hydrogen bond to be disrupted. Comparison of the crystal structures of H93G myoglobin complexed 4‐methylimidazole (4meimd; methylation at carbon 4) and 1‐methylimidazole (1meimd; methylation at the adjacent nitrogen, preventing hydrogen bonding between the imidazole ligand and the protein) shows that the polypeptide, heme, and methylimidazole orientations are the same within error. For 4meimd there appear to be major and minor conformations corresponding to different tautomeric states of the ligand. Conformational heterogeneity is also seen in the hyperfine‐shifted region of the NMR spectrum of 4meimd complexed with high‐spin H93G deoxyMb. The major conformation of the 4meimd ligand and the 1meimd ligand, as seen in the respective crystal structures, are quite similar except that the proximal ligand NH‐to‐Ser92‐OH hydrogen bond is eliminated in the 1meimd complex, and instead the proximal ligand CH is adjacent to the Ser92‐OH. Thus, this system provides a means to eliminate the Mb proximal hydrogen bond in a chemically and structurally conservative way. Proteins 2000;39:278–290. © 2000 Wiley‐Liss, Inc.
Capitalising on intuition and reflection: Making sense of a composer’s creative process

This case study investigated the transformation of intuitive and reflective thinking during a composer’s compositional process. The qualitative data comprised stimulated recall interviews conducted in the composer’s studio during the compositional process and the entire manuscript corpus that the composer created during that process. The results showed the qualitative change in the composer’s intuitive and reflective thinking in the course of the process; within intuitive compositional acts, imagination changed into experimentation and incubation into restructuring, whereas within reflective compositional acts, rule-based reasoning changed into contemplating alternatives. Further, intuitive metacognition decreased while reflective metacognition increased. These changes were explained by concurrent procedures of grounding and rationalisation. In the grounding procedure, the composer substantiated the fuzzy construction of his original ideas (called the Identity Idea by the composer) into aesthetically coherent musical structures that gradually limited the compositional problem space. The rationalisation procedure involved the composer becoming increasingly proficient in the way in which he operated on his musical ideas and materials. After a critical moment, the composer adopted a situation-specific cognitive device called ‘rational intuition’. This ‘rational intuition’ was the composer’s way of creating aesthetic coherence when working fluently, albeit retaining rationality, in an insecure and complex working situation of a creative process. The prerequisites of ‘rational intuition’ were (1) the guidance of a goal-driven cue (i.e. the Identity Idea) as a key determinant and motivational energy for the process; (2) the selection of intuitive and reflective compositional acts to match compositional situations; (3) an expert ability to learn implicitly; and (4) resilience to abeyance.
Metrics for Multivariate Dictionaries

Overcomplete representations and dictionary learning algorithms kept attracting a growing interest in the machine learning community. This paper addresses the emerging problem of comparing multivariate overcomplete representations. Despite a recurrent need to rely on a distance for learning or assessing multivariate overcomplete representations, no metrics in their underlying spaces have yet been proposed. Henceforth we propose to study overcomplete representations from the perspective of frame theory and matrix manifolds. We consider distances between multivariate dictionaries as distances between their spans which reveal to be elements of a Grassmannian manifold. We introduce Wasserstein-like set-metrics defined on Grassmannian spaces and study their properties both theoretically and numerically. Indeed a deep experimental study based on tailored synthetic datasetsand real EEG signals for Brain-Computer Interfaces (BCI) have been conducted. In particular, the introduced metrics have been embedded in clustering algorithm and applied to BCI Competition IV-2a for dataset quality assessment. Besides, a principled connection is made between three close but still disjoint research fields, namely, Grassmannian packing, dictionary learning and compressed sensing.
Weight loss attempts in adults: goals, duration, and rate of weight loss.

OBJECTIVES Although attempted weight loss is common, little is known about the goals and durations of weight loss attempts and the rates of achieved weight loss in the general population. METHODS Data were collected by telephone in 1989 from adults aged 18 years and older in 39 states and the District of Columbia. Analyses were carried out separately for the 6758 men and 14,915 women who reported currently trying to lose weight. RESULTS Approximately 25% of the men respondents and 40% of the women respondents reported that they were currently trying to lose weight. Among men, a higher percentage of Hispanics (31%) than of Whites (25%) or Blacks (23%) reported trying to lose weight. Among women, however, there were no ethnic differences in prevalence. The average man wanted to lose 30 pounds and to weigh 178 pounds; the average woman wanted to lose 31 pounds and to weigh 133 pounds. Black women wanted to lose an average of 8 pounds more than did White women, but Black women's goal weight was 10 pounds heavier. The average rate of achieved weight loss was 1.4 pounds per week for men and 1.1 pounds per week for women; these averages, however, may reflect only the experience of those most successful at losing weight. CONCLUSIONS Attempted weight loss is a common behavior, regardless of age, gender, or ethnicity, and weight loss goals are substantial; however, obesity remains a major public health problem in the United States.
Diversity in intensive English language centres in South Australia: sociocultural approaches to education for students with migrant or refugee backgrounds

ABSTRACT While there is a body of research concerning the education of students with migrant or refugee backgrounds, little of this research focuses on primary school-aged children. In order to address this gap, the current paper utilises data gained from an ethnographic study to consider the challenges and opportunities associated with diverse classrooms designed for students learning English, in which students come from a complex range of backgrounds and may have experienced trauma. The paper provides support for sociocultural learning approaches, whereby students’ own cultural and linguistic background are treated as beneficial to education rather than as obstacles to be overcome.
Dose- and Time-Dependent Association of Smoking and Its Cessation with Glycemic Control and Insulin Resistance in Male Patients with Type 2 Diabetes Mellitus: The Fukuoka Diabetes Registry

Objective Cigarette smoking is an important modifiable risk factor for cardiovascular diseases. However, the effect of smoking and its cessation on glycemic control in diabetic patients has not been fully examined yet. The aim of the present study was to examine the association of smoking status with glycemic level and markers of insulin resistance and secretion in patients with type 2 diabetes mellitus. Research Design and Methods A total of 2,490 Japanese male patients with type 2 diabetes mellitus aged ≥20 years were divided according to smoking status, amount of cigarettes smoked and years since quitting. The associations with glycemic level and markers of insulin resistance and secretion were examined cross-sectionally. Results HbA1c levels increased progressively with increases in both number of cigarettes per day and pack-years of cigarette smoking compared with never smokers (P for trend = 0.001 and <0.001, respectively), whereas fasting plasma glucose did not. On the other hand, HbA1c, but not fasting plasma glucose, decreased linearly with increase in years after smoking cessation (P for trend <0.001). These graded relationships persisted significantly after controlling for the confounders, including total energy intake, current drinking, regular exercise, depressive symptoms, and BMI. In addition, a homeostasis model assessment of insulin resistance and high-sensitivity C-reactive protein also showed similar trends. Conclusions Smoking and its cessation showed dose- and time-dependent relationship with glycemic control and insulin resistance in patients with type 2 diabetes mellitus. These findings may highlight the importance of smoking cessation in the clinical management of diabetes mellitus.
Software-Defined Flow Table Pipeline

Software-Defined Networking (SDN) is revolutionizing data center networks for cloud computing with its ability to enable network virtualization and powerful network resource management that are crucial in any multi-tenant environment. In order to support sophisticated network control logic, the data plane of a switch should have a flexible Flow Table Pipeline (FTP). However, the FTP on state-of-the-art SDN switches is hardware-defined, which greatly limits the advantages of using FTP in cloud computing systems. This paper removes this limitation by introducing software-defined FTP (SDFTP), which provides an extremely flexible FTP as the southbound interface of the SDN control plane. SDFTP offers arbitrary number of pipeline stages and adaptive flow table sizing at runtime by building Software-Defined Flow Tables (SDFTs). Our analysis shows that SDFTP could create 138 times more adaptively sized pipeline stages than the hardware-defined data plane while maintaining comparable performance.
Antiretroviral Therapy Initiation Before, During, or After Pregnancy in HIV-1-Infected Women: Maternal Virologic, Immunologic, and Clinical Response

Background Pregnancy has been associated with a decreased risk of HIV disease progression in the highly active antiretroviral therapy (HAART) era. The effect of timing of HAART initiation relative to pregnancy on maternal virologic, immunologic and clinical outcomes has not been assessed. Methods We conducted a retrospective cohort study from 1997–2005 among 112 pregnant HIV-infected women who started HAART before (N = 12), during (N = 70) or after pregnancy (N = 30). Results Women initiating HAART before pregnancy had lower CD4+ nadir and higher baseline HIV-1 RNA. Women initiating HAART after pregnancy were more likely to receive triple-nucleoside reverse transcriptase inhibitors. Multivariable analyses adjusted for baseline CD4+ lymphocytes, baseline HIV-1 RNA, age, race, CD4+ lymphocyte count nadir, history of ADE, prior use of non-HAART ART, type of HAART regimen, prior pregnancies, and date of HAART start. In these models, women initiating HAART during pregnancy had better 6-month HIV-1 RNA and CD4+ changes than those initiating HAART after pregnancy (−0.35 vs. 0.10 log10 copies/mL, P = 0.03 and 183.8 vs. −70.8 cells/mm3, P = 0.03, respectively) but similar to those initiating HAART before pregnancy (−0.32 log10 copies/mL, P = 0.96 and 155.8 cells/mm3, P = 0.81, respectively). There were 3 (25%) AIDS-defining events or deaths in women initiating HAART before pregnancy, 3 (4%) in those initiating HAART during pregnancy, and 5 (17%) in those initiating after pregnancy (P = 0.01). There were no statistical differences in rates of HIV disease progression between groups. Conclusions HAART initiation during pregnancy was associated with better immunologic and virologic responses than initiation after pregnancy.
Audiovisual Behavior Modeling by Combined Feature Spaces

Great interest is recently shown in behavior modeling, especially in public surveillance tasks. In general it is agreed upon the benefits of use of several input cues as audio and video. Yet, synchronization and fusion of these information sources remains the main challenge. We therefore show results for a feature space combination, which allows for overall feature space optimization. Audio and video features are thereby firstly derived as low-level-descriptors. Synchronization and feature combination is achieved by multivariate time-series analysis. Test-runs on a database of aggressive, cheerful, intoxicated, nervous, neutral, and tired behavior in an airplane situation show a significant improvement over each single modality.
Effects of panduratin A isolated from Kaempferia pandurata ROXB. on the expression of matrix metalloproteinase-9 by porphyromonas gingivalis supernatant-induced KB cells.

Periodontitis is initiated by accumulation of microbial plaque and activation of gingival inflammation through overexpression of matrix metalloproteinases (MMPs), leading to tissue destruction. Natural MMP inhibitors may be developed as therapeutic agents against periodontitis. In this study, panduratin A, a natural bioactive compound isolated from Kaempferia pandurata ROXB. , was used to test its in vitro inhibitory activity against MMP-9 secretion from Porphyromonas gingivalis supernatant-induced human oral epidermoid carcinoma KB cells. Gelatin zymography, Western blot and RT-PCR analyses were performed to evaluate MMP-9 expression. The gelatin zymograms revealed that the main gelatinase secreted by P. gingivalis supernatant-induced KB cells migrated at 92 kDa, representing MMP-9. MMP-9 protein and mRNA levels were significantly decreased after panduratin A treatment (p<0.05). In contrast, panduratin A had no effect on tissue inhibitor of metalloproteinases (TIMP)-1 and TIMP-2 mRNA. Panduratin A also suppressed urokinase type plasminogen activator (uPA) mRNA expression. These results suggest that panduratin A could potentially prevent periodontal inflammation by decreasing the levels of MMP-9 protein and mRNA.
ANALGESIC EFFECTS OF EEG ALPHA-WAVE ENTRAINMENT ON ACUTE AND CHRONIC PAIN

Pharmacological treatments for pain show limited analgesic benefits when compared with placebo. Neuro-modulatory approaches, such as mindfulness meditation and neurofeedback training show more promising effects, but are time consuming and difficult to complete. Neural entrainment provides an almost instantaneous increase in EEG power of the stimulated frequency, achieved with minimal effort through visual flicker stimuli or auditory binaural beats. EEG recorded alpha power displays a reproducible inverse relationship with pain perception. Hence, the main objective of this PhD thesis was to develop an analgesic alpha entrainment intervention: increasing alpha power with the aim to reduce the perception of acute pain in healthy volunteers and chronic pain patients.Prior to attempting to modulate pain, pilot work assessing the ability to entrain alpha power is reported in Chapter 3. A checkerboard stimulus was used to visually entrain frequencies across the alpha band from 7Hz ? 14Hz, resulting in a significant power increase at 10Hz and 11Hz. With the goal to reduce behavioural and electrophysiological responses to a moderately painful stimulus, EEG alpha entrainment at 8Hz, 10Hz and 12Hz through auditory binaural beats (in Chapters 4 and 5), and visual flashing LED goggles (in Chapters 4, 6 and 7) was then attempted. A significant reduction of pain ratings was found following both the visual and the auditory alpha stimulation across all three frequencies in Chapters 4,5 and 6. Chapter 5 revealed a significant alpha power increase following 10Hz and 12Hz auditory stimulation. The laser-evoked potential? s (LEP) N2 peak reduced significantly following 10Hz auditory entrainment and the P2 peak reduced significantly across all auditory entrainment conditions. In Chapter 6, alpha power entrained significantly at 8Hz and 10Hz. The P2 peak reduced significantly following the 10Hz visual stimulation. Source analysis showed the precuneus and posterior cingulate cortex might mediate alpha entrainment-induced reductions in LEPs and pain ratings. The paradigm used in Chapter 6 was repeated in osteoarthritic patients in Chapter 7. Significant reductions in pain ratings were observed following all three alpha stimulation sessions, despite a lack of alpha power increase. A significantly reduced response in the P2 peak was also observed following the 12Hz visual stimulation. Decreases in P2 source activity in the posterior insula suggest a functional role in the reduction of pain intensity triggered by alpha stimulation. A significant reduction in the electrophysiological response and the perception of moderately painful stimuli can be achieved through visual or auditory entrainment across the alpha band range, in both healthy volunteers and osteoarthritic patients. The findings from this PhD thesis provide a solid foundation for further investigation of alpha based neuro-modulation as an analgesic intervention.
Moitree: A Middleware for Cloud-Assisted Mobile Distributed Apps

This paper presents Moitree, the middleware of our Avatar platform for mobile cloud computing. Avatar leverages cloud resources to support fast, scalable, reliable, and energy efficient distributed computing over mobile devices. Each mobile device is augmented by an avatar, a per-user always-on software entity that resides in the cloud and acts as the surrogate of the mobile device, to the extent possible, thus reducing the workload and the demand for storage, bandwidth, and energy on the mobiles. Moitree provides: (1) a novel middleware which allows unmodified apps to execute seamlessly over mobile/avatar pairs with the provision of offloading computation and communication, and (2) a new programming framework to simplify mobile collaborative app development. The programming framework has two key features: (1) user collaborations are modeled using natural group semantics - groups are created dynamically based on context and are hierarchical. (2) data communication is offloaded to the cloud through high-level communication channels. A prototype of Moitree, along with several apps, has been implemented and evaluated on Android devices and on an OpenStack-based cloud running Android x86 avatars.
Optimization of free-moving elements in 2D ultrasound sparse arrays

The non-grid sparse array technique is a promising approach to overcome the connection difficulties of 2D matrix arrays and to partially compensate the energy loss linked to the element number reduction. Being independent from the spatial sampling conditions, this method leads to a significant improvement of the beam pattern when combined to the simulated annealing algorithm. However, in the previous version of this method, the position of the elements cannot be changed during the optimization. In order to add a further degree of freedom and thus to improve the optimization performance, we propose a new strategy in which both element position and apodization can be modified. This new approach improves the sensitivity thanks to a better distribution of the elements on the array footprint.
Platelets from WAS patients show an increased susceptibility to ex vivo phagocytosis

The thrombocytopenia of Wiskott–Aldrich syndrome (WAS) is thought to be due to both reduced platelet production and accelerated platelet consumption. We have previously demonstrated that platelets from WASP-deficient mice are consumed more rapidly in vivo than are WT platelets, and that opsonization accelerates their uptake by bone marrow- derived macrophages more than it does that of WT platelets. Here we asked whether platelets from WAS patients show similar features. We show that ex vivo phagocytosis by activated THP-1 cells of DIO-labeled platelets from a series of WAS or XLT patients is increased in comparison to that of normal control platelets. Using a numerical analysis method, we distinguish this effect from a concurrent effect on the amount of detectable fluorescent signal transferred to the macrophage per phagocytosed platelet. We show that the latter quantity is reduced by platelet WASP deficiency, as might be expected if the fluorescence transferred from these smaller platelets is more rapidly quenched. We are unable to detect a differential effect of opsonization with anti-CD61 antibody on the uptake of WASP(−) vs. WT platelets. However, the high probability of phagocytosis per adsorbed WASP(−) platelet could limit the sensitivity of the assay in this case. We also see no effect of sera from WAS patients on the uptake of normal control platelets, suggesting that in vivo opsonization is not the cause of increased uptake of WASP(−) platelets. Finally, we show little, if any, increase in the reticulated platelet fraction in WAS patients, suggesting that impaired production of reticulated platelets contributes to the thrombocytopenia. Our findings suggest that rapid in vivo platelet consumption contributes significantly to the thrombocytopenia of WAS. They also demonstrate the feasibility of routinely performing functional assays of phagocytosis of small numbers of platelets obtained at remote locations, a method which should be applicable to the study of other types of thrombocytopenia such as ITP.