Miracle-dz/UniFAR-FTUs huggingface dataset:
sfi-independent filamentation in Escherichia coli Is lexA dependent and requires DNA damage for induction

In Escherichia coli, damage to DNA induces the expression of a set of genes known collectively as the SOS response. Part of the SOS response includes genes that repair DNA damage, but another part of the response coordinates DNA replication and septation to prevent untimely cell division. The classic SOS gene product that inhibits cell division is SfiA (or SulA), which binds to FtsZ and prevents septum formation until the DNA damage has been repaired. However, another pathway acts to coordinate DNA replication and cell division when sfiA, or the sfi-dependent pathway, is inoperative. Until recently, little was known of this alternative pathway, which is called the sfi-independent pathway. We report here that sfi-independent filamentation is suppressed by lexA(Ind-) mutations, suggesting that derepression of the LexA regulon is necessary for sfi-independent induction. However, expression of LexA-controlled genes is not sufficient; DNA damage is also required to induce this secondary pathway of cell division inhibition. Furthermore, we postulate that loss of the common regulatory circuitry of the sfi-dependent and sfi-independent pathways by recA or lexA mutants uncouples cell division and DNA replication.
Farming of Plant-Based Veterinary Vaccines and Their Applications for Disease Prevention in Animals

Plants have been studied for the production of pharmaceutical compounds for more than two decades now. Ever since the plant-made poultry vaccine against Newcastle disease virus made a breakthrough and went all the way to obtain regulatory approval, research to use plants for expression and delivery of vaccine proteins for animals was intensified. Indeed, in view of the high production costs of veterinary vaccines, plants represent attractive biofactories and offer many promising advantages in the production of recombinant vaccine proteins. Furthermore, the possibility of conducting immunogenicity and challenge studies in target animals has greatly exaggerated the progress. Although there are no edible plant-produced animal vaccines in the market, plant-based vaccine technology has great potentials. In this review, development, uses, and advantages of plant-based recombinant protein production in various expression platforms are discussed. In addition, examples of plant-based veterinary vaccines showing strong indication in terms of efficacy in animal disease prevention are also described.
Specific Jagged-1 Signal From Bone Marrow Microenvironment Is Required for Endothelial Progenitor Cell Development for Neovascularization

Background— Despite accumulating evidence that proves the pivotal role of endothelial progenitor cells (EPCs) in ischemic neovascularization, the key signaling cascade that regulates functional EPC kinetics remains unclear. Methods and Results— In this report, we show that inactivation of specific Jagged-1 (Jag-1)–mediated Notch signals leads to inhibition of postnatal vasculogenesis in hindlimb ischemia via impairment of proliferation, survival, differentiation, and mobilization of bone marrow–derived EPCs. Bone marrow–derived EPCs obtained from Jag-1−/− mice, but not Delta-like (Dll)-1−/− mice, demonstrated less therapeutic potential for ischemic neovascularization than EPCs from the wild type. In contrast, a gain-of-function study using 3T3 stromal cells overexpressing Notch ligand revealed that Jag-1–mediated Notch signals promoted EPC commitment, which resulted in enhanced neovascularization. The impaired neovascularization in Jag-1−/− mice was profoundly rescued by transplantation of Jag-1–stimulated EPCs. Conclusions— These data indicate that specific Jag-1–derived Notch signals from the bone marrow microenvironment are critical for EPC–mediated vasculogenesis, thus providing an important clue for modulation of strategies for therapeutic neovascularization.
Training and Career Experiences of Women Part-time Workers in a Finance Sector Organisation: Persistent Remnant of the ‘Reserve Army’?

Presenting findings of case study research on employees in a finance sector organisation, this paper explores the linkages between dependant care responsibilities, part-time work and the implications for training and career progression. The study finds that while overtly equitable training and career progression policies exist, the experiences of part-time employees with caring responsibilities are a persistent remnant of the ‘reserve army’ mentality; i.e. women part-time workers are seen as peripheral to the core business and deterred from critical training essential to career progression within the organisation.
OBESITY AND CRITICAL ILLNESS: INSIGHTS FROM ANIMAL MODELS

ABSTRACT Critical illness is a major cause of morbidity and mortality around the world. While obesity is often detrimental in the context of trauma, it is paradoxically associated with improved outcomes in some septic patients. The reasons for these disparate outcomes are not well understood. A number of animal models have been used to study the obese response to various forms of critical illness. Just as there have been many animal models that have attempted to mimic clinical conditions, there are many clinical scenarios that can occur in the highly heterogeneous critically ill patient population that occupies hospitals and intensive care units. This poses a formidable challenge for clinicians and researchers attempting to understand the mechanisms of disease and develop appropriate therapies and treatment algorithms for specific subsets of patients, including the obese. The development of new, and the modification of existing animal models, is important in order to bring effective treatments to a wide range of patients. Not only do experimental variables need to be matched as closely as possible to clinical scenarios, but animal models with pre-existing comorbid conditions need to be studied. This review briefly summarizes animal models of hemorrhage, blunt trauma, traumatic brain injury, and sepsis. It also discusses what has been learned through the use of obese models to study the pathophysiology of critical illness in light of what has been demonstrated in the clinical literature.
Biogeography of bacterioplankton in the tropical seawaters of Singapore.

Knowledge about the biogeography of marine bacterioplankton on the global scale in general and in Southeast Asia in particular has been scarce. This study investigated the biogeography of bacterioplankton community in Singapore seawaters. Twelve stations around Singapore island were sampled on different schedules over 1 year. Using PCR-DNA fingerprinting, DNA cloning and sequencing, and microarray hybridization of the 16S rRNA genes, we observed clear spatial variations of bacterioplankton diversity within the small area of the Singapore seas. Water samples collected from the Singapore Strait (south) throughout the year were dominated by DNA sequences affiliated with Cyanobacteria and Alphaproteobacteria that were believed to be associated with the influx of water from the open seas in Southeast Asia. On the contrary, water in the relatively polluted Johor Strait (north) were dominated by Betaproteobacteria, Gammaproteobacteria, and Bacteroidetes and that were presumably associated with river discharge and the relatively eutrophic conditions of the waterway. Bacterioplankton diversity was temporally stable, except for the episodic surge of Pseudoalteromonas, associated with algal blooms. Overall, these results provide valuable insights into the diversity of bacterioplankton communities in Singapore seas and the possible influences of hydrological conditions and anthropogenic activities on the dynamics of the communities.
Transmembrane cation movements during infection of Lactobacillus lactis by bacteriophage LL-H.

Phage LL-H-induced cation (K+, Na+, Mg2+, Ca2+, Cd2+) movements in Lactobacillus lactis bacteria have been studied. The effects of the m.o. i. and external cation concentration have been quantified. LL-H-induced effluxes showed cation specificity: K+ but practically no Mg2+ was lost during LL-H infection at low and moderate m.o. i. (up to about 100). Simultaneously to K+ efflux, divalent cation influxes were observed. These were dependent on the m.o. i. and on concentrations of external divalent cations and were concomitant with phage DNA transport, as concluded from the timing of the first phage-promoted biochemical changes in host cell metabolism and from electron microscopical observations. Host energy was not mobilized with phage-induced divalent cation influx. Several features of divalent cation influxes support the view that divalent cations have to be cotransported into the cell as counterions of LL-H DNA. Phage DNA associated with divalent cations may be the basic feature of the divalent cation dependence of LL-H infection.
A Survey on Challenges of Software Project Management

Recent surveys indicate that software projects have still high failure rates. In order to increase the odds of success, we have to identify the challenges and determine the causes. Management issues, rather than technological issues, are mostly the causes of these failures. We identified 17 possible areas in which the projects may have been challenged. In this study, we present our findings based on a survey on challenges of management of software projects. We conducted the survey in 2007 among 78 software practitioners regarding their last projects. The participants are from different geographical regions of the world.
A Historical Mission in the Accountability Era

The case study is an analysis of a state performance funding policy at a public historically Black college and university (HBCU). The policy attaches state funding to HBCU performance on measures like graduation rates and equity measures like the reduction in achievement gaps between Black and non-Black students. Participants liked that the policy helped the institution to become more outcome minded, but were critical of the equity measures and their relationship with the state system of higher education. The article addresses how the HBCU’s mission was addressed in the policy and its plans for responding that includes focusing on Latino students.
Effect of whole body vibration frequency on neuromuscular activity in ACL-deficient and healthy males

Whole-body vibration (WBV) has been shown to enhance muscle activity via reflex pathways, thus having the potential to contrast muscle weakness in individuals with rupture of the anterior cruciate ligament (ACL). The present study aimed to compare the magnitude of neuromuscular activation during WBV over a frequency spectrum from 20 to 45 Hz between ACL-deficient and healthy individuals. Fifteen males aged 28±4 with ACL rupture and 15 age-matched healthy males were recruited. Root mean square (RMS) of the surface electromyogram from the vastus lateralis in both limbs was computed during WBV in a static half-squat position at 20, 25, 30, 35, 40 and 45 Hz, and normalized to the RMS while maintaining the half-squat position without vibration. The RMS of the vastus lateralis in the ACL-deficient limb was significantly greater than in the contralateral limb at 25, 30, 35 and 40 Hz (P<0.05) and in both limbs of the healthy participants (dominant limb at 25, 30, 35, 40 and 45 Hz, P<0.05; non dominant limb at 20, 25, 30, 35, 40 and 45 Hz, P<0.05). The greater neuromuscular activity in the injured limb compared to the uninjured limb of the ACL-deficient patients and to both limbs of the healthy participants during WBV might be due to either augmented excitatory or reduced inhibitory neural inflow to motoneurons of the vastus lateralis through the reflex pathways activated by vibratory stimuli. The study provides optimal WBV frequencies which might be used as reference values for ACL-deficient patients.
Duplication Models for Biological Networks

Are biological networks different from other large complex networks? Both large biological and nonbiological networks exhibit power-law graphs (number of nodes with degree k, N(k) approximately k(-beta)), yet the exponents, beta, fall into different ranges. This may be because duplication of the information in the genome is a dominant evolutionary force in shaping biological networks (like gene regulatory networks and protein-protein interaction networks) and is fundamentally different from the mechanisms thought to dominate the growth of most nonbiological networks (such as the Internet). The preferential choice models used for nonbiological networks like web graphs can only produce power-law graphs with exponents greater than 2. We use combinatorial probabilistic methods to examine the evolution of graphs by node duplication processes and derive exact analytical relationships between the exponent of the power law and the parameters of the model. Both full duplication of nodes (with all their connections) as well as partial duplication (with only some connections) are analyzed. We demonstrate that partial duplication can produce power-law graphs with exponents less than 2, consistent with current data on biological networks. The power-law exponent for large graphs depends only on the growth process, not on the starting graph.
PR based output voltage regulation for harmonic compensation under islanded mode of microgrid with magnitude restoration

This study examines the P+ multi resonant based voltage control for the voltage harmonics compensation under the islanded mode of a microgrid. In islanded mode, the inverter is defined as a voltage source to supply the full local load demand without a connection to the grid. On the other hand, the output voltage waveform is distorted by the negative and zero sequence and current harmonics due to the unbalanced and nonlinear loads. In this paper, P+ multi resonant controller has been used to compensate the voltage harmonics. The gain tuning method is assessed by the analysis of the tendency of controller as the variation of gain. In addition, this study analyzes the slight voltage magnitude drop due to the practical form of the P+ multi resonant, and proposes the counter method to solve this problem by adding the PI based voltage restoration method. Furthermore, the proposed PR based harmonics compensation method has been extended to the droop based parallel operation which also supplies the nonlinear load. Finally, the proposed methods to compensate for the voltage harmonics are verified through the PSiM simulation and experimental results.
Mind Your Blocks: On the Stealthiness of Malicious BGP Hijacks

Some recent research presented evidence of blocks of IP addresses being stolen by BGP hijackers to launch spam campaigns (35). This was the first time BGP hijacks were seen in the wild. Since then, only a very few anecdotal cases have been reported as if hackers were not interested in running these attacks. However, it is a common belief among network operators and ISPs that these attacks could be taking place but, so far, no one has produced evidence to back up that claim. In this paper, we analyse 18 months of data collected by an infrastructure specifically built to answer that question: are intentional stealthy BGP hijacks routinely taking place in the Internet? The identification of what we believe to be more than 2,000 malicious hijacks leads to a positive answer. The lack of ground truth is, of course, a problem but we managed to get confirmation of some of our findings thanks to an ISP unwittingly involved in hijack cases we have spotted. This paper aims at being an eye opener for the community by shedding some light on this undocumented threat. We also hope that it will spur new research to understand why these hijacks are taking place and how they can be mitigated. Depending on how BGP attacks are carried out, they can be very disruptive for the whole Internet and should be looked at very closely. As of today, as much as 20% of the whole IPv4 address space is currently allocated but not publicly announced, which makes it potentially vulnerable to such malicious BGP hijacks.
The vagal innervation of the gut and immune homeostasis

The central nervous system interacts dynamically with the immune system to modulate inflammation through humoral and neural pathways. Recently, in animal models of sepsis, the vagus nerve (VN) has been proposed to play a crucial role in the regulation of the immune response, also referred to as the cholinergic anti-inflammatory pathway. The VN, through release of acetylcholine, dampens immune cell activation by interacting with α-7 nicotinic acetylcholine receptors. Recent evidence suggests that the vagal innervation of the gastrointestinal tract also plays a major role controlling intestinal immune activation. Indeed, VN electrical stimulation potently reduces intestinal inflammation restoring intestinal homeostasis, whereas vagotomy has the reverse effect. In this review, we will discuss the current understanding concerning the mechanisms and effects involved in the cholinergic anti-inflammatory pathway in the gastrointestinal tract. Deeper investigation on this counter-regulatory neuroimmune mechanism will provide new insights in the cross-talk between the nervous and immune system leading to the identification of new therapeutic targets to treat intestinal immune disease.
Preoperative ultrasound guided percutaneous axillary biopsy in breast cancer patients: fine needle aspiration cytology versus core biopsy.

AIM The aim of this study is to compare the diagnostic accuracy in detecting axillary node metastases between preoperative ultrasound with percutaneous core biopsy or fine needle aspiration cytology, in patients with breast cancer. MATERIAL AND METHODS All cases with newly diagnosed ipsilateral primary breast cancer that underwent axillary ultrasound guided biopsies in a 2 year period were reviewed and the biopsy outcome was compared to the final histopathology from sentinel lymph node biopsy or axillary node dissection. Comparison was also attempted in a subgroup including only patients who underwent one method and in a second subgroup of patients who had both techniques performed. RESULTS Within the total population results are in favor of core biopsy which correlates statistically significantly with the final histology after excluding neoadjuvant related false negatives. Within the single modality subgroup results are again in favor of core biopsy which again correlates statistically significantly with the final histology. Within the combined modality subgroup results demonstrate equal diagnostics but neither method demonstrates statistically significant diagnostic success. DISCUSSION The results of the study are generally in favour of core biopsy which tends currently to override fine needle aspiration cytology. Only few studies have directly compared the two methods and a great variability exists in the results of the different studies. CONCLUSIONS A case-match cohort study is advised to accurately compare the diagnostic value of the two methods. Until then the decision will be based on the radiologist's experience. KEY WORDS Breast cancer, Diagnostic accuracy, Percutaneous axillary biopsy.
Reliable and Timely Event Notification for Publish/Subscribe Services Over the Internet

The publish/subscribe paradigm is gaining attention for the development of several applications in wide area networks (WANs) due to its intrinsic time, space, and synchronization decoupling properties that meet the scalability and asynchrony requirements of those applications. However, while the communication in a WAN may be affected by the unpredictable behavior of the network, with messages that can be dropped or delayed, existing publish/subscribe solutions pay just a little attention to addressing these issues. On the contrary, applications such as business intelligence, critical infrastructures, and financial services require delivery guarantees with strict temporal deadlines. In this paper, we propose a framework that enforces both reliability and timeliness for publish/subscribe services over WAN. Specifically, we combine two different approaches: gossiping, to retrieve missing packets in case of incomplete information, and network coding, to reduce the number of retransmissions and, consequently, the latency. We provide an analytical model that describes the information recovery capabilities of our algorithm and a simulation-based study, taking into account a real workload from the Air Traffic Control domain, which evidences how the proposed solution is able to ensure reliable event notification over a WAN within a reasonable bounded time window.
Optimizing cerebellar transcranial direct current stimulation for visuomotor learning - anterior versus posterior lobe of cerebellum

This study sought to investigate two-electrode montages for the application of anodal transcranial direct current stimulation (atDCS) over ipsilateral cerebellar hemisphere during visuomotor learning of myoelectric visual pursuit using electromyogram (EMG) from gastrocnemius (GAS) muscle. The atDCS montages were selected based on computational modeling to target electric field strength at the anterior lobe (AL) or posterior lobe (PL) or AL+PL of the cerebellum. AL atDCS resulted in a statistically significant (p<0.05) decrease in RT post-intervention than baseline when compared to PL atDCS and AL+PL atDCS. However, only AL+PL atDCS resulted in a significant decrease in RMSE post-intervention than baseline. Here, optimizing the direction of the electric field relative to cerebellar peduncles may be relevant.
Subsurface imaging of carbon nanotube networks in polymers with DC-biased multifrequency dynamic atomic force microscopy

The characterization of dispersion and connectivity of carbon nanotube (CNT) networks inside polymers is of great interest in polymer nanocomposites in new material systems, organic photovoltaics, and in electrodes for batteries and supercapacitors. We focus on a technique using amplitude modulation atomic force microscopy (AM-AFM) in the attractive regime of operation, using both single and dual mode excitation, which upon the application of a DC tip bias voltage allows, via the phase channel, the in situ, nanoscale, subsurface imaging of CNT networks dispersed in a polymer matrix at depths of 10–100 nm. We present an in-depth study of the origins of phase contrast in this technique and demonstrate that an electrical energy dissipation mechanism in the Coulomb attractive regime is key to the formation of the phase contrast which maps the spatial variations in the local capacitance and resistance due to the CNT network. We also note that dual frequency excitation can, under some conditions, improve the contrast for such samples. These methods open up the possibility for DC-biased amplitude modulation AFM to be used for mapping the variations in local capacitance and resistance in nanocomposites with conducting networks.