Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization of the type III secretion sorting platform of Shigella flexneri

Significance Many infectious bacteria such as Shigella and Salmonella use type III secretion machines, also called injectisomes, to transfer virulence proteins into eukaryotic host cells. A cytoplasmic sorting platform is required for effector selection and assembly of the needle but has not been visualized in any bacteria. We combine advanced imaging and genetic techniques to visualize the frozen-hydrated diarrheal pathogen Shigella flexneri and reveal the intact type III secretion machine and its interaction with a host cell for the first time to our knowledge. The structures characterized herein provide new insights into the mechanisms underlying type III secretion and pathogenesis and also highlight the major distinctions from the evolutionarily related bacterial flagellum. Bacterial type III secretion machines are widely used to inject virulence proteins into eukaryotic host cells. These secretion machines are evolutionarily related to bacterial flagella and consist of a large cytoplasmic complex, a transmembrane basal body, and an extracellular needle. The cytoplasmic complex forms a sorting platform essential for effector selection and needle assembly, but it remains largely uncharacterized. Here we use high-throughput cryoelectron tomography (cryo-ET) to visualize intact machines in a virulent Shigella flexneri strain genetically modified to produce minicells capable of interaction with host cells. A high-resolution in situ structure of the intact machine determined by subtomogram averaging reveals the cytoplasmic sorting platform, which consists of a central hub and six spokes, with a pod-like structure at the terminus of each spoke. Molecular modeling of wild-type and mutant machines allowed us to propose a model of the sorting platform in which the hub consists mainly of a hexamer of the Spa47 ATPase, whereas the MxiN protein comprises the spokes and the Spa33 protein forms the pods. Multiple contacts among those components are essential to align the Spa47 ATPase with the central channel of the MxiA protein export gate to form a unique nanomachine. The molecular architecture of the Shigella type III secretion machine and its sorting platform provide the structural foundation for further dissecting the mechanisms underlying type III secretion and pathogenesis and also highlight the major structural distinctions from bacterial flagella.
A random early demotion and promotion marker for assured services

The differentiated services (DiffServ) model, proposed to evolve the current best-effort Internet to a quality-of-service-aware Internet, provides packet level service differentiation on a per-hop basis. The end-to-end service differentiation may be provided by extending the per-hop behavior over multiple network domains through service level agreements between domains. The edge routers of each of the domains monitor the aggregate flow of the incoming packets and demote packets when the aggregate incoming traffic exceeds the negotiated interdomain service agreement. A demoted packet may encounter other edge routers on its path that have sufficient resources to route the packet with its original marking. In this paper, we propose a random early demotion and promotion (REDP) technique that works at the aggregate traffic level and allows (1) fair demotion of packets belonging to different flows, and (2) easy and fair detection and promotion of the demoted packets. Using early and random decisions on packets REDP ensures fairness in promotion and demotion. It uses a three color marking mechanism, reserving one color fur differentiating between a demoted packet and a packet with the original out-of-profile marking. We experiment with the proposed REDP scheme using the ns2 simulator for both TCP and UDP streams. The results demonstrate the fairness of REDP scheme in demoting and promoting packets. Furthermore, we show a variety of results that demonstrates that REDP provides better assured services compared to the previously proposed RIO scheme with or without the provision of promotion.
Outbreaks of Disease Suspected of Being Due to Human Monkeypox Virus Infection in the Democratic Republic of Congo in 2001

ABSTRACT Seven outbreaks of disease characterized by a pustular rash and suspected to have been caused by human monkeypox virus were investigated. The outbreaks occurred between February and August 2001 in the province of Equateur in the Democratic Republic of Congo. The outbreaks involved a total of 31 persons and caused five deaths. Specimens from 14 patients were available and were analyzed by electron microscopy, virus isolation, and PCR assays specific for monkeypox virus and varicella-zoster virus. We provide evidence that two outbreaks were indeed caused by monkeypox virus (16 cases, with four deaths), that in two outbreaks both monkeypox and varicella-zoster virus were involved (seven cases, with one death), and that two outbreaks were cases of chickenpox caused by infection with varicella-zoster virus (six cases, with no deaths). In one outbreak, no evidence for either monkeypox or chickenpox was found (two cases, with no deaths).
Evaluation of Fungal Growth on Olive-Mill Wastewaters Treated at High Temperature and by High-Pressure Homogenization

Reuse of olive mill wastewaters (OMWWs) in agriculture represents a significant challenge for health and safety of our planet. Phytotoxic compounds in OMWW generally prohibit use of untreated OMWWs for agricultural irrigation or direct discharge into surface waters. However, pretreated OMWW can have positive effects on chemical and microbiological soil characteristics, to fight against fungal soil-borne pathogens. Low amounts of OMWW following thermal (TT-OMWW) and high-pressure homogenization (HPH-OMWW) pretreatments counteracted growth of some of 12 soil-borne and/or pathogenic fungi examined. With fungal growth measured as standardized change in time to half maximum colony diameter, Δτ, overall, HPH-OMWW showed increased bioactivity, as increased mean Δτ from 3.0 to 4.8 days. Principal component analysis highlighted two fungal groups: Colletotrichum gloeosporioides, Alternaria alternata, Sclerotium rolfsii, and Rosellinia necatrix, with growth strongly inhibited by the treated OMWWs; and Aspergillus ochraceus and Phaeoacremonium parasiticum, with stimulated growth by the treated OMWWs. As a non-thermal treatment, HPH-OMWW generally shows improved positive effects, which potentially arise from preservation of the phenols.
Eastern Bering Sea - 2005

The very warm winters of the late 1970s and 1980s were followed by cooler winters in the 1990s. This cooling was likely a result of a shift in the Arctic Oscillation and hence a tendency for higher sea-level pressure (SLP) over the Bering Sea. Since 1998, negative SLP anomalies have prevailed, which is indicative of greater Pacific influence and consistent with generally milder winters. The winter of 2004 was anomalously warm (although somewhat colder than the winter of 2003), with temperatures typical of the first decade after the 1977 regime shift. Ice cover in the vicinity of Mooring 2 was below the 1989-2004 average almost all season long, except during a cold spell in late March-early April. Spring air and sea surface temperatures were much above normal.
A horse’s locomotor signature: COP path determined by the individual limb

Introduction Ground reaction forces in sound horses with asymmetric hooves show systematic differences in the horizontal braking force and relative timing of break-over. The Center Of Pressure (COP) path quantifies the dynamic load distribution under the hoof in a moving horse. The objective was to test whether anatomical asymmetry, quantified by the difference in dorsal wall angle between the left and right forelimbs, correlates with asymmetry in the COP path between these limbs. In addition, repeatability of the COP path was investigated. Methods A larger group (n = 31) visually sound horses with various degree of dorsal hoof wall asymmetry trotted three times over a pressure mat. COP path was determined in a hoof-bound coordinate system. A relationship between correlations between left and right COP paths and degree of asymmetry was investigated. Results Using a hoof-bound coordinate system made the COP path highly repeatable and unique for each limb. The craniocaudal patterns are usually highly correlated between left and right, but the mediolateral patterns are not. Some patterns were found between COP path and dorsal wall angle but asymmetry in dorsal wall angle did not necessarily result in asymmetry in COP path and the same could be stated for symmetry. Conclusion This method is a highly sensitive method to quantify the net result of the interaction between all of the forces and torques that occur in the limb and its inertial properties. We argue that changes in motor control, muscle force, inertial properties, kinematics and kinetics can potentially be picked up at an early stage using this method and could therefore be used as an early detection method for changes in the musculoskeletal apparatus.
A comparison of imputation strategies in cluster randomized trials with missing binary outcomes

In cluster randomized trials, clusters of subjects are randomized rather than subjects themselves, and missing outcomes are a concern as in individual randomized trials. We assessed strategies for handling missing data when analysing cluster randomized trials with a binary outcome; strategies included complete case, adjusted complete case, and simple and multiple imputation approaches. We performed a simulation study to assess bias and coverage rate of the population-averaged intervention-effect estimate. Both multiple imputation with a random-effects logistic regression model or classical logistic regression provided unbiased estimates of the intervention effect. Both strategies also showed good coverage properties, even slightly better for multiple imputation with a random-effects logistic regression approach. Finally, this latter approach led to a slightly negatively biased intracluster correlation coefficient estimate but less than that with a classical logistic regression model strategy. We applied these strategies to a real trial randomizing households and comparing ivermectin and malathion to treat head lice.
Eysenck's Challenge to Psychotherapy: A View of the Effects 50 Years on

Hans Eysenck was head of Psychology at the Maudsley Hospital during the heyday of Sir Aubrey Lewis. Eysenck established the Maudsley as a powerhouse of behaviourism. His clear and lucid style of writing, and his incisive mind, made him a formidable advocate. In 1952, he offered a challenge to the field of psychotherapy. In considering a number of outcome studies he
Effects of Alcohol on Brain‐Tissue Impedance in Animals and Man

&NA; The effect of blood alcohol levels to 240 mg. /lOO ml. on the impedance of the amygdala, hippocampus, lateral geniculate bodies (normal and degenerated, 1 year after striatal cortex ablation), and the midbrain reticular formation, has been examined in cats. The characteristic response to alcohol was a fall in both the reactive and resistive components of impedance. No regional differences were found. There was no significant change in impedance in the degenerated lateral geniculate bodies. The pes hippocampus of 2 human subjects showed the same response to alcohol as the normal cat brain.
Unambiguous Computations and Locally Deenable Acceptance Types: Expanded Version

Hertrampf's locally de nable acceptance types show that many complexity classes can be de ned in terms of polynomial time bounded NTM's with simple local conditions on the nodes of its computation tree, rather than global concepts like number of accepting paths etc. We introduce a modi cation of Hertrampf's locally de nable acceptance types which allows to get a larger number of characterizable complexity classes. Among others the newly characterizable classes are UP and ModZkP . It is shown how di erent types of oracle access, e.g., guarded access, can be characterized by this model. This sheds new light on the discussion on how to access unambiguous computation. We present simple functions that describe precisely objects of current research as the unambiguous oracle, alternation, and promise hierarchies. We exhibit the new class UAP which seems to be an unambiguous analogue of Wagner's rP . UAP (and thus rP) contains Few and is currently the smallest class known with this property.
Early Results with Precision Abstraction: Using Data-flow Analysis to Improve the Scalability of Model Checking

This paper presents a new state space reduction technique that applies to model checking of software. The new technique, precision abstraction, borrows ideas from dataflow analysis to identify procedures that can be analyzed context-insensitively without affecting the accuracy of the verification of a given property. These context-insensitive procedures can then be represented with fewer states than would be needed context-sensitive analysis. Preliminary results indicate that the number of transitions in the analysis prescribed by our approach is at least 155 times fewer than the exhaustive analysis a model checker would otherwise perform.
What do Women want in a Moral Theory

When I finished reading Carol Gilligan's "In Another Voice", I asked myself the obvious question for a philosopher reader, namely what differences one should expect in the moral philosophy done by women, supposing Gilligan's sample of women representative, and supposing her analysis of their moral attitudes and moral development to be correct. Should one expect them to want to produce moral theories, and if so, what sort of moral theories? How will any moral theories they produce differ from those produced by men? Obviously one does not have to make this an entirely a priori and hypothetical question. One can look and see what sort of contributions women have made to moral philosophy. Such a look confirms, I think, Gilligan's findings. What one finds is a bit different in tone and approach from the standard sort of moral philosophy as done by men following in the footsteps of the great moral philosophers (all men). Generalizations are extremely rash, but when I think of Philippa Foot's work on the moral virtues, of Elizabeth Anscombe's work on intention and on modern moral philosophy, of Iris Murdoch's philosophical writings, of Ruth Barcan Marcus' work on moral dilemmas, of the work of the radical feminist moral philosophers who are not content with orthodox Marxist lines of thought, of Jenny Teichman's book on Illegitimacy, of Susan Wolf's recent articles, of Claudia Card's essay on mercy, Sabina Lovilbond's recent book, Gabriele Taylor's work on pride, love and on integrity, Cora Diamond's and Mary Midgeley's work on our attitude to animals, Sissela Bok's work on lying and on secrecy, Virginia Held's work, the work of Alison Jaggar, Marilyn Frye, and many others, I seem to hear a different voice from the standard moral philosophers' voice. I hear the voice Gilligan heard, made reflective and philosophical. What women want in moral
Sternoclavicular Septic Arthritis: Review of 180 Cases

Abstract: We review 170 previously reported cases of sternoclavicular septic arthritis, and report 10 new cases. The mean age of patients was 45 years; 73% were male. Patients presented with chest pain (78%) and shoulder pain (24%) after a median duration of symptoms of 14 days. Only 65% were febrile. Bacteremia was present in 62%. Common risk factors included intravenous drug use (21%), distant site of infection (15%), diabetes mellitus (13%), trauma (12%), and infected central venous line (9%). No risk factor was found in 23%. Serious complications such as osteomyelitis (55%), chest wall abscess or phlegmon (25%), and mediastinitis (13%) were common. Staphylococcus aureus was responsible for 49% of cases, and is now the major cause of sternoclavicular septic arthritis in intravenous drug users. Pseudomonas aeruginosa infection in injection drug users declined dramatically with the end of an epidemic of pentazocine abuse in the 1980s. Sternoclavicular septic arthritis accounts for 1% of septic arthritis in the general population, but 17% in intravenous drug users, for unclear reasons. Bacteria may enter the sternoclavicular joint from the adjacent valves of the subclavian vein after injection of contaminated drugs into the upper extremity, or the joint may become infected after attempted drug injection between the heads of the sternocleidomastoid muscle. Computed tomography or magnetic resonance imaging should be obtained routinely to assess for the presence of chest wall phlegmon, retrosternal abscess, or mediastinitis. If present, en-bloc resection of the sternoclavicular joint is indicated, possibly with ipsilateral pectoralis major muscle flap. Empiric antibiotic therapy may need to cover methicillin-resistant Staphylococcus aureus (MRSA).
Multiple-antenna signal constellations for fading channels

In this paper, we design multiple-antenna signal constellations for a Rayleigh flat-fading channel unknown to the receiver. It is shown that good signal constellations correspond to packings with large minimum distances in complex Grassmannian space. We describe a numerical optimization procedure for finding such packings. The corresponding signal constellations improve significantly upon previously best-known signal constellations.
Effectiveness of Prism Adaptation in Neglect Rehabilitation: A Controlled Trial Study

Background and Purpose— This study was conducted to investigate the effectiveness on neglect recovery of a 2-week treatment based on prism adaptation (PA) in comparison to an analogous visuomotor training performed without prisms, ie, neutral pointing (NP). Methods— Twenty neglect patients were divided into 2 matched groups, one was submitted to PA (PA group) and the other to NP (NP group) for 10 daily sessions over a period of 2 weeks. After the end of NP treatment, the patients in the NP group were also submitted to PA treatment. Neglect was assessed before and after each treatment and 1 month after the end of the PA treatment. Results— Visuospatial abilities improved after both PA and NP treatment; however, the improvement was significantly higher in the patients in the PA group than in the patients in the NP group. Moreover, when the patients in the NP group were submitted to PA, they further improved up to the level reached by patients in the PA group, ie, to nonpathological scores. Long-lasting beneficial effects of PA were confirmed 1 month from the end of treatment. Conclusion— The leftward recalibration of sensorimotor reference frames induced by PA is effective to obtain proper neglect recovery, although visuomotor training based on pointing might partially improve neglect symptoms.
HMGB1 Is Associated with Atherosclerotic Plaque Composition and Burden in Patients with Stable Coronary Artery Disease

Objectives The role of inflammation in atherosclerosis is widely appreciated. High mobility group box 1 (HMGB1), an injury-associated molecular pattern molecule acting as a mediator of inflammation, has recently been implicated in the development of atherosclerosis. In this study, we sought to investigate the association of plasma HMGB1 with coronary plaque composition in patients with suspected or known coronary artery disease (CAD). Design HMGB1, high sensitive troponin T (hsTnT) and high sensitive C-reactive protein (hsCRP) were determined in 152 consecutive patients with suspected or known stable CAD who underwent clinically indicated 256-slice coronary computed tomography angiography (CCTA). Using CCTA, we assessed 1) coronary calcification, 2) non-calcified plaque burden and 3) the presence of vascular remodeling in areas of non-calcified plaques. Results Using univariate analysis, hsCRP, hsTnT and HMGB1 as well as age, and atherogenic risk factors were associated with non-calcified plaque burden (r = 0.21, p = 0.009; r = 0.48, p<0.001 and r = 0.34, p<0.001, respectively). By multivariate analysis, hsTnT and HMGB1 remained independent predictors of the non-calcified plaque burden (r = 0.48, p<0.01 and r = 0.34, p<0.001, respectively), whereas a non-significant trend was noticed for hs-CRP (r = 0.21, p = 0.07). By combining hsTnT and HMGB1, a high positive predictive value for the presence of non-calcified and remodeled plaque (96% and 77%, respectively) was noted in patients within the upper tertiles for both biomarkers, which surpassed the positive predictive value of each marker separately. Conclusions In addition to hs-TnT, a well-established cardiovascular risk marker, HMGB1 is independently associated with non-calcified plaque burden in patients with stable CAD, while the predictive value of hs-CRP is lower. Complementary value was observed for hs-TnT and HMGB1 for the prediction of complex coronary plaque.
Frequency-Based 3D Reconstruction of Transparent and Specular Objects

3D reconstruction of transparent and specular objects is a very challenging topic in computer vision. For transparent and specular objects, which have complex interior and exterior structures that can reflect and refract light in a complex fashion, it is difficult, if not impossible, to use either passive stereo or the traditional structured light methods to do the reconstruction. We propose a frequency-based 3D reconstruction method, which incorporates the frequency-based matting method. Similar to the structured light methods, a set of frequency-based patterns are projected onto the object, and a camera captures the scene. Each pixel of the captured image is analyzed along the time axis and the corresponding signal is transformed to the frequency-domain using the Discrete Fourier Transform. Since the frequency is only determined by the source that creates it, the frequency of the signal can uniquely identify the location of the pixel in the patterns. In this way, the correspondences between the pixels in the captured images and the points in the patterns can be acquired. Using a new labelling procedure, the surface of transparent and specular objects can be reconstructed with very encouraging results.
Nurses' competence in genetics: a mixed method systematic review.

AIM To ascertain the extent to which nurses are achieving the core competences in genetics appropriate for nursing practice. BACKGROUND There is an increasing focus on genetics in nursing, and relevant core competences have been developed. However, it is unclear whether nurses are achieving these competences. DATA SOURCES Four databases (CINAHL, Medline, The Allied and Complementary Medicine Database, and British Nursing Index) were searched. Hand searching of relevant reference lists and author names was also conducted. DESIGN Systematic review. REVIEW METHODS The systematic review was undertaken using methods described by the Centre for Reviews and Dissemination (University of York, 2008). Research studies published in English between January 2000-January 2011 reporting data focussing on nurse competence in genetics were eligible for inclusion. Data were abstracted for inclusion in a table and subjected to thematic analysis: due to diversity of studies, a meta-analysis was not performed. RESULTS Of 269 papers retrieved, 13 were eligible for inclusion. There were five main themes: knowledge, experience in using skills, ethical practice, perceived relevance, and confidence. Although the majority of participants believed genetics was relevant to their role, their knowledge of genetic concepts was generally poor; however, most studies measured self-reported knowledge rather than assessing actual knowledge. CONCLUSIONS There is little evidence on this topic, but it does appear from the available evidence that nurses are not demonstrating the competences needed to offer holistic health care to people with genetic conditions. Pre- and post-registration programmes must be enhanced to include genetic health care.