Miracle-dz/UniFAR-FTUs huggingface dataset:
Human papillomavirus infection in women with the human immunodeficiency virus type-1

Septicemia continues to be a major cause of neonatal mortality and morbidity worldwide. Aim: To study the incidence, microbial profile and emergence of extended spectrum beta lactamases mediated resistance (ESBL) in neonatal septicemia in relation to gestational age and birth weight. This is a prospective study of 1647 babies suspected of neonatal septicemia based on symptomatology and clinical diagnosis. Evaluated data included: age, sex, birth weight, type of isolated pathogen, and antibiotic sensitivity. Gram negative bacteria were the predominant organisms to be isolated. Klebsiella spp 232 (26.5%) was the predominant organism followed by E. coli 92(10.5%), and Acinetobacter 54(6.2%). Among Gram-positive bacteria, Staphylococcus aureus 176 (20.1%) was the predominant followed by coagulase negative Staphylococci 118(13.6%). Preterm babies were highly significantly more susceptible to infection than term babies (61.9% vs 40.4%; P<0.001). Klebsiella sps is the predominant organism (36.7% & 23.8%) isolated among both preterm male and female babies followed by Staphylococcus aureus (14.4% & 14.7%). Among term babies Staphylococcus aureus (32.6%) was the predominant among the male babies followed by E.coli (23.5%) and Staphylococcus aureus (33.3%) was the predominant among female babies followed by CoNS (26.9%). Among the low birth weight babies, Klebsiella sps was isolated in 41.9% and in normal weight babies, Staphylococcus aureus (42.9%) was the predominant among the male babies and Klebsiella sps (32.3%) was the predominant among female babies Multidrug resistant organisms were found to be most pathogenic. 32.8% of gram negative bacilli were ESL producer Klebsiella pneumoniae was the predominant ESL producer 47(43.9%) followed by E.coli 15 (14.0), and Pseudomonas aeruginosa 11(10.3%). AmpC production was seen in 18 (6.2%) of the isolates
Magnetic field amplification and saturation in turbulence behind a relativistic shock

We have investigated via two-dimensional relativistic MHD simulations the long-term evolution of turbulence created by a relativistic shock propag ating through an inhomogeneous medium. In the postshock region, magnetic field is strongly a mplified by turbulent motions triggered by preshock density inhomogeneities. Using a long-simulation box we have followed the magnetic-field amplification until it is fully deve loped and saturated. The turbulent velocity is sub-relativistic even for a strong shock. Magne tic-field amplification is controled by the turbulent motion and saturation occurs when the magnetic energy is comparable to the turbulent kinetic energy. Magnetic-field amplification and saturation depend on the initial strength and direction of the magnetic field in the presh ock medium, and on the shock strength. If the initial magnetic field is perpendicular to t he shock normal, the magnetic field is first compressed at the shock and then can be amplified by tur bulent motion in the postshock region. Saturation occurs when the magnetic energy becomes comparable to the turbulent kinetic energy in the postshock region. If the initial magneti c field in the preshock medium is strong, the postshock region becomes turbulent but signific ant field amplification does not occur. If the magnetic energy after shock compression is larger than the turbulent kinetic energy in the postshock region, significant field amplification does not occur. We discuss possible applications of our results to gamma-ray bursts and active galactic nuclei.
Investigating the dental toolkit of primates based on food mechanical properties: Feeding action does matter

Although conveying an indisputable morphological and behavioral signal, traditional dietary categories such as frugivorous or folivorous tend to group a wide range of food mechanical properties together. Because food/tooth interactions are mostly mechanical, it seems relevant to investigate the dental morphology of primates based on mechanical categories. However, existing mechanical categories classify food by its properties but cannot be used as factors to classify primate dietary habits. This comes from the fact that one primate species might be adapted to a wide range of food mechanical properties. To tackle this issue, what follows is an original framework based on action‐related categories. The proposal here is to classify extant primates based on the range of food mechanical properties they can process through one given action. The resulting categories can be used as factors to investigate the dental tools available to primates. Furthermore, cracking, grinding, and shearing categories assigned depending on the hardness and the toughness of food are shown to be supported by morphological data (3D relative enamel thickness) and topographic data (relief index, occlusal complexity, and Dirichlet normal energy). Inferring food mechanical properties from dental morphology is especially relevant for the study of extinct primates, which are mainly documented by dental remains. Hence, we use action‐related categories to investigate the molar morphology of an extinct colobine monkey Mesopithecus pentelicus from the Miocene of Pikermi, Greece. Action‐related categories show contrasting results compared with classical categories and give us new insights into the dietary adaptations of this extinct primate. Finally, we provide some possible directions for future research aiming to test action‐related categories. In particular, we suggest acquiring more data on mechanically challenging fallback foods and advocate the use of other food mechanical properties such as abrasiveness. The development of new action‐related dental metrics is also crucial for primate dental studies.
Mid size cliques are more common in real world networks than triangles

Abstract Real world networks typically have large clustering coefficients. The clustering coefficient can be interpreted to be the result of a triangle closing mechanism. We have here enumerated cliques and maximal cliques in multiple networks to show that real world networks have a high number of large cliques. While triangles are more frequent than expected, large cliques are much more over-expressed, and the largest difference between real world networks and their random counterpart occurs in many networks at clique sizes of 5–7, and not at a size of 3. This does not result from the existence of few very large cliques, since a similar feature is observed when studying only maximal cliques (cliques that are not contained in other larger cliques). Moreover, when the large cliques are removed, triangles are often under-expressed. In all networks studied but one, all node members of large cliques produce a single connected component, which represent the central “core” of the network. The observed clique distribution can be explained by multiple models, mainly hidden variables model, such as the gravitation model, or the collapse of bipartite networks. These models can explain other properties of these networks, including the sub-graph distribution and the distance distribution of the networks. This suggests that node connectivity in real world networks may be determined by the similarity between the contents of the networks' nodes. This is in contrast with models of network formation that incorporate only the properties of the network, and not the internal properties of the nodes.
The efficacy and feasibility of aquatic physiotherapy for people with Parkinson’s disease: a systematic review

Abstract Purpose: To critically evaluate the literature regarding the efficacy and feasibility of aquatic physiotherapy in people with Parkinson’s disease. Method: Relevant studies were identified through searches in nine health-related databases. Two independent reviewers assessed study quality using either the PEDro scale or a customised tool for safety and feasibility. Results: Database searches yielded 88 articles, of which 10 met the inclusion criteria. Studies varied greatly in methodology, quality, interventions and outcome measures. Study quality was generally low in items reporting on safety precautions, adverse events, attrition, and adherence. Results suggest that aquatic physiotherapy may have a positive effect on motor symptoms, quality of life and balance. Conclusions: Aquatic physiotherapy may improve aspects of motor performance, quality of life and balance in people with Parkinson’s disease, however, it remains unclear whether it is a safe and feasible treatment modality. The development of standardised outcome measures for people with Parkinson’s disease (unified Parkinson’s disease rating scale and Parkinson’s disease questionnaire-39) would aid study comparability and validate study outcomes. As safety criteria was grossly underreported, guidelines for mandatory reporting of safety criteria are essential to make conclusions regarding the feasibility of aquatic physiotherapy for people with Parkinson’s disease. Implications for Rehabilitation Aquatic physiotherapy may be a beneficial treatment modality for people with Parkinson’s disease. A minimum data set that includes the unified Parkinson’s disease rating scale and Parkinson’s disease questionnaire 39 is required to aid future meta-analysis and to allow more definitive conclusions to be made regarding aquatic physiotherapy for people with Parkinson’s disease. People with Parkinson’s disease are a vulnerable population, where safety within an aquatic physiotherapy program needs to be well documented and addressed.
Influence of Antipsychotic Drugs on Human Endogenous Retrovirus (HERV) Transcription in Brain Cells

Human endogenous retroviruses (HERVs) have been associated with various neurological and neuropsychiatric disorders. Transcripts and proteins of at least three HERV groups, HERV-W, ERV9 and HERV-K(HML-2) have been detected repeatedly in brain samples or cerebrospinal fluid of patients with schizophrenia suggesting that alterations in HERV activity may play a role in etiopathogenesis. Current therapies otherwise include neuroleptics and/or antidepressants that may induce epigenetic alterations and thus influence HERV expression. To investigate the effects of these drugs on HERV transcriptional activity, HERV expression profiles of a broad range of human brain cell lines treated with valproic acid (VPA), haloperidol, risperidone, and clozapine were analyzed using a retrovirus-specific microarray and qRT-PCR. Investigation of 52 HERV subgroups revealed upregulation of several class I and class II HERV elements by VPA in a dose-dependent manner. The strongest effect was observed on HERV-W and ERV9 groups in the human glioblastoma cell lines SK-N-SH and SK-N-MC, respectively. The transcript level of HERV-K(HML-2) elements was not influenced. Transcription of HERV-W, ERV9 and HERV-K(HML-2) taxa was further quantified in postmortem brain samples of patients with schizophrenia, bipolar disorders and a healthy control group with regard to their medication. Patients with schizophrenia showed a significantly higher HERV-W transcription associated with VPA treatment. However in case of ERV9, enhanced transcript levels could not be explained solely by VPA treatment, since a slight increase was also found in untreated patients compared to healthy controls. HERV-K(HML-2) elements appeared to be upregulated in some patients with bipolar disorders independent from medication. In conclusion, these results suggest that antipsychotic medication may contribute to increased expression of distinct HERV taxa in patients with neuropsychiatric diseases.
Thymosin-beta4 modulates corneal matrix metalloproteinase levels and polymorphonuclear cell infiltration after alkali injury.

PURPOSE Corneal alkali injury is highly caustic, and present clinical therapies are limited. The purpose of this study was to investigate the ability of thymosin-beta4 (Taubeta4) to promote healing in an alkali injury model and the mechanisms involved in that process. METHODS Corneas of BALB/c mice were injured with NaOH, irrigated copiously with PBS, and treated topically with either Tbeta4 or PBS twice daily. At various time points after injury (PI), corneas from the Tbeta4- versus the PBS-treated group were examined for polymorphonuclear leukocyte (PMN) infiltration, chemokine, and matrix metalloproteinase (MMP)/tissue inhibitor of metalloproteinase (TIMP) expression. RESULTS Tbeta4-treated corneas demonstrated improved corneal clarity at day 7 PI. Whereas Tbeta4 decreased corneal MMP-2 and -9 and MT6-MMP levels after alkali injury, no change in TIMP-1 and -2 expression was detected. Tbeta4 treatment also decreased corneal KC (CXCL1) and macrophage inflammatory protein (MIP)-2 chemokine expression and PMN infiltration. Immunohistochemistry studies demonstrated MMP-9 expression at the leading edge of the epithelial wound, in the the limbus (containing stem cells), and in stromal PMNs. CONCLUSIONS Tbeta4 treatment decreases corneal inflammation and modulates the MMP/TIMP balance and thereby promotes corneal wound repair and clarity after alkali injury. These results suggest that Tbeta4 may be useful clinically to treat severe inflammation-mediated corneal injuries.
Some physical properties of milk powders

Data for some physical properties of regular and instantised skim milk powder (SMP), whole milk powder (WMP) and fat-filled milk powder (FFMP) are presented; bulk density (packed, aerated, average and working), compressibility, angle of repose, dispersibility in air, particle size distribution (sieve analysis, coefficient of uniformity and distribution index) and reconstitution properties (wettability, dispersibility and solubility index). Aerated bulk density ranged from 0.30-0.62 g/cm3 compared with the range 0.44-0.85 g/cm3 for packed bulk density and compressibility ranged from 32-40%. Mean particle size (median value of cumulative distribution) ranged from 85 pm for regular SMPs to 230-250 |im for FFMPs. SMPs were more dispersible in air (18-20%) than the fat-containing powders (7-11%). The angle of repose ranged from 33? -38? for SMPs to 40? -58? for the fat-containing powders and in a pilot-scale conveying trial the skim powders were observed to be more flowable. In general, conveying under the experimental conditions did not result in particle size reduction and the reconstitution properties of the instant powders were not adversely affected.
Synchronization Strings: Efficient and Fast Deterministic Constructions over Small Alphabets

Synchronization strings are recently introduced by Haeupler and Shahrasbi (STOC 2017) in the study of codes for correcting insertion and deletion errors (insdel codes). They showed that for any parameter $\varepsilon>0$, synchronization strings of arbitrary length exist over an alphabet whose size depends only on $\varepsilon$. Specifically, they obtained an alphabet size of $O(\varepsilon^{-4})$, which left an open question on where the minimal size of such alphabets lies between $\Omega(\varepsilon^{-1})$ and $O(\varepsilon^{-4})$. In this work, we partially bridge this gap by providing an improved lower bound of $\Omega(\varepsilon^{-3/2})$, and an improved upper bound of $O(\varepsilon^{-2})$. We also provide fast explicit constructions of synchronization strings over small alphabets. Further, along the lines of previous work on similar combinatorial objects, we study the extremal question of the smallest possible alphabet size over which synchronization strings can exist for some constant $\varepsilon < 1$. We show that one can construct $\varepsilon$-synchronization strings over alphabets of size four while no such string exists over binary alphabets. This reduces the extremal question to whether synchronization strings exist over ternary alphabets.
Kaposi's Sarcoma-Associated Herpesvirus Reduces Cellular Myeloid Differentiation Primary-Response Gene 88 (MyD88) Expression via Modulation of Its RNA

ABSTRACT Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is a human gammaherpesvirus associated with several human malignancies. The replication and transcription activator (RTA) is necessary and sufficient for the switch from KSHV latency to lytic replication. Interleukin 1 (IL-1) is a major mediator for inflammation and plays an important role in both innate and adaptive immunity. Myeloid differentiation primary response gene 88 (MyD88) is an essential adaptor molecule for IL-1 as well as most Toll-like receptor signaling. In this study, we identified a novel mechanism by which KSHV interferes with host inflammation and immunity. KSHV RTA specifically reduces the steady-state protein levels of MyD88, and physiological levels of MyD88 are downregulated during KSHV lytic replication when RTA is expressed. The N-terminal region of RTA is required for the reduction of MyD88. Additional studies demonstrated that RTA targets MyD88 expression at the RNA level, inhibits RNA synthesis of MyD88, and may bind MyD88 RNA. Finally, RTA inhibits IL-1-mediated activation of NF-κB. Because IL-1 is abundant in the KS microenvironment and inhibits KSHV replication, this work may expand our understanding of how KSHV evades host inflammation and immunity for its survival in vivo. IMPORTANCE MyD88 is an important molecule for IL-1-mediated inflammation and Toll-like receptor (TLR) signaling. This work shows that KSHV inhibits MyD88 expression through a novel mechanism. KSHV RTA may bind to MyD88 RNA, suppresses RNA synthesis of MyD88, and inhibits IL-1-mediated signaling. This work may expand our understanding of how KSHV evades host inflammation and immunity.
Learning to Play General Video-Games via an Object Embedding Network

Deep reinforcement learning (DRL) has proven to be an effective tool for creating general video-game AI. However most current DRL video-game agents learn end-to-end from the video-output of the game, which is superfluous for many applications and creates a number of additional problems. More importantly, directly working on pixel-based raw video data is substantially distinct from what a human player does. In this paper, we present a novel method which enables DRL agents to learn directly from object information. This is obtained via use of an object embedding network (OEN) that compresses a set of object feature vectors of different lengths into a single fixed-length unified feature vector representing the current game-state and fulfills the DRL simultaneously. We evaluate our OEN-based DRL agent by comparing to several state-of-the-art approaches on a selection of games from the GVG-AI Competition. Experimental results suggest that our object-based DRL agent yields performance comparable to that of those approaches used in our comparative study.
Clinical Outcome of Electrophysiologically Guided Ablation for Nonparoxysmal Atrial Fibrillation Using a Novel Real-Time 3-Dimensional Mapping Technique: Results From a Prospective Randomized Trial

Background: Clinical outcomes after ablation of persistent atrial fibrillation remain suboptimal. Identification of AF drivers using a novel integrated mapping technique may be crucial to ameliorate the clinical outcome. Methods and Results: Persistent AF patients were prospectively enrolled to undergo high-density electrophysiological mapping to identify repetitive-regular activities (RRas) before modified circumferential pulmonary vein (PV) ablation. They have been randomly assigned (1:1 ratio) to ablation of RRa followed by modified circumferential PV ablation (mapping group; n=41) or modified circumferential PV ablation alone (control group; n=40). The primary end point was freedom from arrhythmic recurrences at 1 year. In total, 81 persistent AF patients (74% male; mean age, 61.7±10.6 years) underwent mapping/ablation procedure. The regions exhibiting RRa were 479 in 81 patients (5.9±2.4 RRa per patient): 232 regions in the mapping group (n=41) and 247 in the control group (n=40). Overall, 185 of 479 (39%) RRas were identified within the PVs, whereas 294 of 479 (61%) in non-PV regions. Mapping-guided ablation resulted in higher arrhythmia termination rate when compared with conventional strategy (25/41, 61% versus 12/40, 30%; P<0.007). Total radiofrequency duration (P=0.38), mapping (P=0.46), and fluoroscopy times (P=0.69) were not significantly different between the groups. No major procedure-related adverse events occurred. After 1 year, 73.2% of mapping group patients were free from recurrences versus 50% of control group (P=0.03). Conclusions: Targeted ablation of regions showing RRa provided an adjunctive benefit in terms of arrhythmia freedom at 1-year follow-up in the treatment of persistent AF. These findings might support a patient-tailored strategy in subjects with nonparoxysmal AF and should be confirmed by additional larger, randomized, multicenter studies. Clinical Trial Registration: URL: https://www.clinicaltrials. gov. Unique identifier NCT02571218.
Fragile X Syndrome: The GABAergic System and Circuit Dysfunction

Fragile X syndrome (FXS) is a neurodevelopmental disorder characterized by intellectual disability, sensory hypersensitivity, and high incidences of autism spectrum disorders and epilepsy. These phenotypes are suggestive of defects in neural circuit development and imbalances in excitatory glutamatergic and inhibitory GABAergic neurotransmission. While alterations in excitatory synapse function and plasticity are well-established in Fmr1 knockout (KO) mouse models of FXS, a number of recent electrophysiological and molecular studies now identify prominent defects in inhibitory GABAergic transmission in behaviorally relevant forebrain regions such as the amygdala, cortex, and hippocampus. In this review, we summarize evidence for GABAergic system dysfunction in FXS patients and Fmr1 KO mouse models alike. We then discuss some of the known developmental roles of GABAergic signaling, as well as the development and refinement of GABAergic synapses as a framework for understanding potential causes of mature circuit dysfunction. Finally, we highlight the GABAergic system as a relevant target for the treatment of FXS.
256 Shades of gray: uncertainty and diagnostic error in radiology

Abstract Radiologists practice in an environment of extraordinarily high uncertainty, which results partly from the high variability of the physical and technical aspects of imaging, partly from the inherent limitations in the diagnostic power of the various imaging modalities, and partly from the complex visual-perceptual and cognitive processes involved in image interpretation. This paper reviews the high level of uncertainty inherent to the process of radiological imaging and image interpretation vis-à-vis the issue of radiological interpretive error, in order to highlight the considerable degree of overlap that exists between these. The scope of radiological error, its many potential causes and various error-reduction strategies in radiology are also reviewed.