Miracle-dz/UniFAR-FTUs huggingface dataset:
The telework experience in Japan

When top executives in Japanese organizations were asked to predict upcoming devel-opments over the next 10 to 20 years, many highlighted telework as having the poten-tial to become one of the main work styles for white-collar workers. The numerouspotential benefits of telework for individuals, organizations, and society as a whole arewell understood; however, adoption and diffusion of telework have been considerablyslower in Japan compared with other industrialized countries [1]. According to aSatellite Office Association of Japan estimate [7], there are just over 900,000 tele-workers in Japan, and this number includes individuals who telework as little as oncemonthly or less. Lack of appropriate telework adoption guidelines and misunder-standings by middle management appear to be playing a major role in the slow adop-tion of telework in Japan [2, 5]. Many in middle management are simply afraid of it,and while members of upper management tend to be curious, most are waiting forsomeone else to take the lead. In recent years, several major Japanese companies haveemerged as quite successful in adopting telework. In this article, five successful telework adoption cases and four not-so-successfulcases are examined and compared in terms of the four telework phases of adoption:inception, testing, implementation, and future planning. We begin by defining sev-eral telework terms used here (For a more comprehensive discussion of telework clas-sification, see [3]). • Telecommuting involves working at home during regular work hours. • A satellite office refers to an office located in close proximity to group of workers’residences. • A mobile worker is one who works at a customer site or some other location cho-sen by him or her. • A spot office is generally used by mobile workers as a temporary office space out-side of their primary office. A company typically designates several desks in anexisting branch office as a spot office.
Computational methods for feedback control in damped gyroscopic second-order systems

Two new computationally viable algorithms are proposed for partial pole-placement and eigenstructure assignment in damped gyroscopic matrix second-order systems. The algorithms can be implemented with only a partial knowledge of the spectrum and the corresponding eigenvectors of the associated open-loop quadratic matrix pencil. Mathematical results are proved to guarantee that there will be no-spillover effects; that is, it is shown mathematically that the large-number of eigenvalues and eigenvectors that need to remain unchanged will not be effected by feedback. Furthermore, the algorithms work directly in second-order setting allowing them to exploit structures such as sparsity, band, symmetry etc. These practical features of the algorithms make them ideally suited for real-life applications such as control and stabilization of large flexible space structures.
Proteins Involved in Motility and Sperm-Egg Interaction Evolve More Rapidly in Mouse Spermatozoa

Proteomic studies of spermatozoa have identified a large catalog of integral sperm proteins. Rapid evolution of these proteins may underlie adaptive changes of sperm traits involved in different events leading to fertilization, although the selective forces underlying such rapid evolution are not well understood. A variety of selective forces may differentially affect several steps ending in fertilization, thus resulting in a compartmentalized adaptation of sperm proteins. Here we analyzed the evolution of genes associated to various events in the sperm’s life, from sperm formation to sperm-egg interaction. Evolutionary analyses were performed on gene sequences from 17 mouse strains whose genomes have been sequenced. Four of these are derived from wild Mus musculus, M. domesticus, M. castaneus and M. spretus. We found a higher proportion of genes exhibiting a signature of positive selection among those related to sperm motility and sperm-egg interaction. Furthermore, sperm proteins involved in sperm-egg interaction exhibited accelerated evolution in comparison to those involved in other events. Thus, we identified a large set of candidate proteins for future comparative analyses of genotype-phenotype associations in spermatozoa of species subjected to different sexual selection pressures. Adaptive evolution of proteins involved in motility could be driven by sperm competition, since this selective force is known to increase the proportion of motile sperm and their swimming velocity. On the other hand, sperm proteins involved in gamete interaction could be coevolving with their egg partners through episodes of sexual selection or sexual conflict resulting in species-specific sperm-egg interactions and barriers preventing interspecies fertilization.
Mycoplasma genitalium: from Chrysalis to Multicolored Butterfly

SUMMARY The history, replication, genetics, characteristics (both biological and physical), and factors involved in the pathogenesis of Mycoplasma genitalium are presented. The latter factors include adhesion, the influence of hormones, motility, possible toxin production, and immunological responses. The preferred site of colonization, together with current detection procedures, mainly by PCR technology, is discussed. The relationships between M. genitalium and various diseases are highlighted. These diseases include acute and chronic nongonococcal urethritis, balanoposthitis, chronic prostatitis, and acute epididymitis in men and urethritis, bacterial vaginosis, vaginitis, cervicitis, pelvic inflammatory disease, and reproductive disease in women. A causative relationship, or otherwise strong association, between several of these diseases and M. genitalium is apparent, and the extent of this, on a subjective basis, is presented; also provided is a comparison between M. genitalium and two other genital tract-orientated mollicutes, namely, Mycoplasma hominis, the first mycoplasma of human origin to be discovered, and Ureaplasma species. Also discussed is the relationship between M. genitalium and infertility and also arthritis in both men and women, as is infection in homosexual and immunodeficient patients. Decreased immunity, as in HIV infections, may enhance mycoplasmal detection and increase disease severity. Finally, aspects of the antimicrobial susceptibility and resistance of M. genitalium, together with the treatment and possible prevention of mycoplasmal disease, are discussed.
Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities

Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic experimental structure solving, despite essential to the understanding of these functions, is often difficult and expensive. Docking approaches that have been developed for proteins are often challenging to adapt for RNA because of its inherent flexibility and the structural data available being relatively scarce. In this study we adapted the RosettaDock protocol for protein-RNA complexes both at the nucleotide and atomic levels. Using a genetic algorithm-based strategy, and a non-redundant protein-RNA dataset, we derived a RosettaDock scoring scheme able not only to discriminate but also score efficiently docking decoys. The approach proved to be both efficient and robust for generating and identifying suitable structures when applied to two protein-RNA docking benchmarks in both bound and unbound settings. It also compares well to existing strategies. This is the first approach that currently offers a multi-level optimized scoring approach integrated in a full docking suite, leading the way to adaptive fully flexible strategies.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1008 Physical Activity and Alzheimer ' s Disease Measurements , Observations and Subjective Experiences

Cedervall, Y. 2014. Physical Activity and Alzheimer's Disease. Measurements, Observations and Subjective Experiences. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1008. 82 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-8967-0. Gait disturbances such as slow walking speed and step-to-step variability have been reported among people with mild Alzheimer’s disease (AD) and as risk factors for functional decline, dependency, and falls. Additionally, AD-related emotional reactions and decreased initiative can lead to physical inactivity. The aims of this thesis, therefore, were to explore how the ability to be physically active is affected in the early years of AD, and how people with mild AD and their cohabitants reason about physical activity as part of their everyday life. To meet the aims, an approach inspired by mixed methods research was used, covering measurements, observations and subjective experiences. Data were collected from different sources in parallel. Participants with mild AD were recruited at the Memory Clinic, Uppsala University Hospital. In Study I, a case study with two couples in which one member had AD, in-depth interviews and participating interviews were performed. Physical activity such as walking was viewed as a meaningful routine improving well-being. Participants were positive about making adjustments to enable physical activity. In Study II, the 25 participants with AD showed a significant lower walking capacity (10 m comfortable walk test, 6-minute walk test, Timed-up-and-Go test) at baseline compared to controls. The decline continued during the subsequent two years. The influence of a cognitive task on walking was distinct, despite this, participants maintained a health-promoting level of physical activity during the two-year study-period. In Study III, gait testing in the motor laboratory of 21 participants with AD showed a marked impact on gait parameters (e.g. slowed speed, decreased step length) by a cognitive task. Additionally, specific dual-task gait disturbances were frequent. In Study IV, in-depth interviews with 14 participants with AD indicated that physical activity was viewed as a meaningful activity, used as a means to maintain well-being and selfhood, and contributed to continuity in life. In conclusion, walking capacity deteriorates and declines in the early stages of AD. A simple cognitive task can have a substantially negative impact on walking already in mild AD. In contrast, people with AD can also gain “self-promoting benefits” from physical activity beyond the common health-promoting benefits.
Platelet Function Testing-Guided Antiplatelet Therapy

Cardiovascular diseases are the leading cause of death in the Western world. Several factors have led to the increase in vascular disorders, including the aging population, unhealthy lifestyles, increasing rates of diabetes and raised lipids, and further risk factors resulting in inflammation and calcification of the vascular endothelium. Activated platelets in damaged blood vessels can trigger arterial thrombus formation, leading to vascular occlusion with subsequent organ hypoperfusion and clinical manifestation of myocardial infarction, stroke, or peripheral artery disease. Platelet inhibitors such as aspirin and clopidogrel (Plavix® and generics) are prescribed as primary or secondary prevention to attenuate chronic platelet activation. However, a significant proportion of patients do not respond adequately to uniform antiplatelet treatment. These ‘non-responders’ have an increased risk for stent thrombosis, stroke, and other ischemic complications. Platelet function (PF) tests can identify these patients thus enabling physicians to offer personalized and alternative treatment strategies. Recent alternatives to clopidogrel include prasugrel (Efient®) and ticagrelor (Brilique®) – that are both more potent than clopidogrel but also more expensive and associated with a higher risk of bleeding complications. Given these drawbacks, PF testing might help clinicians to prescribe optimal antiplatelet agent to maximize patient safety and efficacy while minimizing costs. While randomized studies using different test systems have left clinicians puzzled about the medical value of tailored antiplatelet therapy, accumulated evidence from recent studies on tailored antiplatelet therapies and the association with improved outcomes have now resulted in a consensus expert opinion for the specific adoption of PF diagnostics into clinical practice.
Academic Coupled Dictionary Learning for Sketch-based Image Retrieval

In the last few years, the query-by-visual-example paradigm gained popularity, specially for content based retrieval systems. As sketches represent a natural way of expressing a synthetic query, recent research efforts focused on developing algorithmic solutions to address the sketch-based image retrieval (SBIR) problem. Within this context, we propose a novel approach for SBIR that, unlike previous methods, is able to exploit the visual complexity inherently present in sketches and images. We introduce academic learning, a paradigm in which the sample learning order is constructed both from the data, as in self-paced learning, and from partial curricula. We propose an instantiation of this paradigm within the framework of coupled dictionary learning to address the SBIR task. We also present an efficient algorithm to learn the dictionaries and the codes, and to pace the learning combining the reconstruction error, the prior knowledge suggested by the partial curricula and the cross-domain code coherence. In order to evaluate the proposed approach, we report an extensive experimental validation showing that the proposed method outperforms the state-of-the-art in coupled dictionary learning and in SBIR on three different publicly available datasets.
Long-Term Glucose Infusion Increases Arterial Pressure in Dogs With Cyclooxygenase-2 Inhibition

A series of studies has shown that long-term infusion of insulin and glucose does not increase mean arterial pressure (MAP) in dogs, but we have shown that the same infusion protocol or infusion of glucose alone increases arterial pressure in rats. This study tested the hypothesis that infusing glucose alone in dogs, with all insulin derived from endogenous secretion, would increase arterial pressure. Because fructose feeding in dogs also has been shown not to cause hypertension and because we have shown that prostaglandin production increases during insulin and glucose infusion, this study also tested whether prostaglandins prevent the pressor response in dogs. Dogs were instrumented and assigned in random crossover design to long-term cyclooxygenase-2 (COX-2) inhibition. After baseline measurements, glucose was infused in all dogs for 6 days (≈500 g/d IV). Plasma insulin increased 3- to 4-fold and blood glucose increased significantly in both groups. The MAP (measured 24 h/d) response in control dogs was variable but on average tended to increase, although not significantly. In the dogs with COX-2 inhibition, however, MAP increased significantly to a peak of 9±2 mm Hg and an average of 6±1 mm Hg above control. There was significant sodium and volume retention during glucose infusion and a significant increase in glomerular filtration rate, but there were no between-group differences. Plasma renin activity increased only in the control group. This is the first study to report a long-term pressor response with glucose infusion and hyperinsulinemia in dogs, and it suggests that the inability to detect this relationship previously was due to prostaglandins.
Resistance to Antimicrobials Mediated by Efflux Pumps in Staphylococcus aureus

Resistance mediated by efflux has been recognized in Staphylococcus aureus in the last few decades, although its clinical relevance has only been recognized recently. The existence of only a few studies on the individual and overall contribution of efflux to resistance phenotypes associated with the need of well-established methods to assess efflux activity in clinical isolates contributes greatly to the lack of solid knowledge of this mechanism in S. aureus. This study aims to provide information on approaches useful to the assessment and characterization of efflux activity, as well as contributing to our understanding of the role of efflux to phenotypes of antibiotic resistance and biocide tolerance in S. aureus clinical isolates. The results described show that efflux is an important contributor to fluoroquinolone resistance in S. aureus and suggest it as a major mechanism in the early stages of resistance development. We also show that efflux plays an important role on the reduced susceptibility to biocides in S. aureus, strengthening the importance of this long neglected resistance mechanism to the persistence and proliferation of antibiotic/biocide-resistant S. aureus in the hospital environment.
Akt1 in Osteoblasts and Osteoclasts Controls Bone Remodeling

Bone mass and turnover are maintained by the coordinated balance between bone formation by osteoblasts and bone resorption by osteoclasts, under regulation of many systemic and local factors. Phosphoinositide-dependent serine-threonine protein kinase Akt is one of the key players in the signaling of potent bone anabolic factors. This study initially showed that the disruption of Akt1, a major Akt in osteoblasts and osteoclasts, in mice led to low-turnover osteopenia through dysfunctions of both cells. Ex vivo cell culture analyses revealed that the osteoblast dysfunction was traced to the increased susceptibility to the mitochondria-dependent apoptosis and the decreased transcriptional activity of runt-related transcription factor 2 (Runx2), a master regulator of osteoblast differentiation. Notably, our findings revealed a novel role of Akt1/forkhead box class O (FoxO) 3a/Bim axis in the apoptosis of osteoblasts: Akt1 phosphorylates the transcription factor FoxO3a to prevent its nuclear localization, leading to impaired transactivation of its target gene Bim which was also shown to be a potent proapoptotic molecule in osteoblasts. The osteoclast dysfunction was attributed to the cell autonomous defects of differentiation and survival in osteoclasts and the decreased expression of receptor activator of nuclear factor-κB ligand (RANKL), a major determinant of osteoclastogenesis, in osteoblasts. Akt1 was established as a crucial regulator of osteoblasts and osteoclasts by promoting their differentiation and survival to maintain bone mass and turnover. The molecular network found in this study will provide a basis for rational therapeutic targets for bone disorders.
Ion binding in the Open HCN Pacemaker Channel Pore: Fast Mechanisms to Shape “Slow” Channels

IH pacemaker channels carry a mixed monovalent cation current that, under physiological ion gradients, reverses at ∼−34 mV, reflecting a 4:1 selectivity for K over Na. However, IH channels display anomalous behavior with respect to permeant ions such that (a) open channels do not exhibit the outward rectification anticipated assuming independence; (b) gating and selectivity are sensitive to the identity and concentrations of externally presented permeant ions; (c) the channels' ability to carry an inward Na current requires the presence of external K even though K is a minor charge carrier at negative voltages. Here we show that open HCN channels (the hyperpolarization-activated, cyclic nucleotide sensitive pore forming subunits of IH) undergo a fast, voltage-dependent block by intracellular Mg in a manner that suggests the ion binds close to, or within, the selectivity filter. Eliminating internal divalent ion block reveals that (a) the K dependence of conduction is mediated via K occupancy of site(s) within the pore and that asymmetrical occupancy and/or coupling of these sites to flux further shapes ion flow, and (b) the kinetics of equilibration between K-vacant and K-occupied states of the pore (10–20 μs or faster) is close to the ion transit time when the pore is occupied by K alone (∼0.5–3 μs), a finding that indicates that either ion:ion repulsion involving Na is adequate to support flux (albeit at a rate below our detection threshold) and/or the pore undergoes rapid, permeant ion-sensitive equilibration between nonconducting and conducting configurations. Biophysically, further exploration of the Mg site and of interactions of Na and K within the pore will tell us much about the architecture and operation of this unusual pore. Physiologically, these results suggest ways in which “slow” pacemaker channels may contribute dynamically to the shaping of fast processes such as Na-K or Ca action potentials.
Oral Susceptibility of Singapore Aedes (Stegomyia) aegypti (Linnaeus) to Zika Virus

Background Zika virus (ZIKV) is a little known flavivirus that caused a major outbreak in 2007, in the South-western Pacific Island of Yap. It causes dengue-like syndromes but with milder symptoms. In Africa, where it was first isolated, ZIKV is mainly transmitted by sylvatic Aedes mosquitoes. The virus has also been isolated from Ae. aegypti and it is considered to be the vector involved in the urban transmission of the virus. Transmission of the virus by an African strain of Ae. aegypti has also been demonstrated under laboratory conditions. The aim of the present study is to describe the oral susceptibility of a Singapore strain of Ae. aegypti to ZIKV, under conditions that simulate local climate. Methodology/Principal Findings To assess the receptivity of Singapore's Ae. aegypti to the virus, we orally exposed a local mosquito strain to a Ugandan strain of ZIKV. Upon exposure, fully engorged mosquitoes were maintained in an environmental chamber set at 29°C and 70–75% RH. Eight mosquitoes were then sampled daily from day 1 to day 7, and subsequently on days 10 and 14 post exposure (pe). The virus titer of the midgut and salivary glands of each mosquito were determined using a tissue culture infectious dose50 (TCID50) assay. High midgut infection and salivary gland dissemination rates were observed. By day 5 after the infectious blood meal, ZIKV was found in the salivary glands of more than half of the mosquitoes tested (62%); and by day 10, all mosquitoes were potentially infective. Conclusions/Significance This study showed that Singapore's urban Ae. aegypti are susceptible and are potentially capable of transmitting ZIKV. The virus could be established in Singapore should it be introduced. Nevertheless, Singapore's current dengue control strategy is applicable to control ZIKV.
“Mini‐array” transcriptional analysis of the Listeria monocytogenes lecithinase operon as a class project: A student investigative molecular biology laboratory experience *

This report describes a molecular biotechnology‐based laboratory curriculum developed to accompany an undergraduate genetics course. During the course of a semester, students researched the pathogen, developed a research question, designed experiments, and performed transcriptional analysis of a set of genes that confer virulence to the food‐borne pathogen, Listeria monocytogenes. Gene fragments were amplified via PCR and utilized in “mini‐arrays,” a dot‐blot‐based format suitable for the simultaneous transcriptional analysis of multiple genes. The project provides exposure to a wide range of molecular techniques and can be easily modified for variations in class size. Data are generated at various steps of the process, allowing for student interpretation, troubleshooting, and assessment opportunities.