Miracle-dz/UniFAR-FTUs huggingface dataset:
Breastfeeding in the time of Zika: a systematic literature review

Background The disease Zika is considered as emergent. The infection can be acquired through different routes: a bite from the Aedes mosquito, sexual contact, from mother to child during pregnancy and by blood transfusion. The possibility of Zika transmission through human lactation has been considered. Zika is a disease of great concern for public health because it has been associated with neonatal and postnatal microcephaly, among other birth defects. Objectives To review published evidence of the probable transmission of Zika through human lactation. Data sources Electronic databases: Cochrane Central Register of Controlled Trials, EBSCO, Gale, Science Direct, Scopus, US National Library of Medicine (PubMed) and Web of Science. World Health Organization and Centers for Disease Control and Prevention web pages. Study eligibility criteria To be eligible, studies of any design had to provide primary data of human breast milk as a potential fluid for the transmission of Zika, or primary or secondary follow-up data of infants with at least one previous published study that complied with the first criterion of eligibility. Participants Studies about women with suspected, probable or confirmed Zika during pregnancy, or the postnatal period and beyond. Studies about infants who breastfeed directly from the breast or where fed with the expressed breast milk of the suspected, probable or confirmed women with Zika. Results This study only chose data from research papers; no patients were taken directly by the authors. A total of 1,146 were screened and nine studies were included in the qualitative synthesis, from which a total of 10 cases were identified, with documented follow-up in three of these cases. Through the timing of maternal Zika infection, five cases were classified as prenatal (time before delivery), one as immediate postnatal (period from 0 to 4 days after birth); no cases were classified as medium postnatal (period from 5 days to 8 weeks after birth); two were classified as long postnatal (period from 8 weeks to 6 months after birth) and two as beyond six months after birth. Conclusion Human milk may be considered as a potentially infectious fluid, but we found no currently documented studies of the long-term complications in infants up to 32 months of age, with suspected, probable or confirmed Zika through human lactation, or evidence with respect to the human pathophysiology of the infection acquired through human lactation. In the light of the studies reviewed here, the World Health Organization recommendation of June 29th 2016, remains valid: “the benefits of breastfeeding for the infant and mother outweigh any potential risk of Zika virus transmission through breast milk. ”
Can threatened species adapt in a restored habitat? No expected evolutionary response in lay date for the New Zealand hihi

Many bird species have been observed shifting their laying date to earlier in the year in response to climate change. However, the vast majority of these studies were performed on non‐threatened species, less impacted by reduced genetic diversity (which is expected to limit evolutionary response) as a consequence of genetic bottlenecks, drift and population isolation. Here, we study the relationship between lay date and fitness, as well as its genetic basis, to understand the evolutionary constraints on phenology faced by threatened species using a recently reintroduced population of the endangered New Zealand passerine, the hihi (Notiomystis cincta). A large discrepancy between the optimal laying date and the mode of laying date creates a strong selection differential of −11.24. The impact of this discrepancy on fitness is principally mediated through survival of offspring from hatchling to fledgling. This discrepancy does not seem to arise from a difference in female quality or a trade‐off with lifetime breeding success. We find that start of breeding season depends on female age and average temperature prior to the breeding season. Laying date is not found to be significantly heritable. Overall, our research suggests that this discrepancy is a burden on hihi fitness, which will not be resolved through evolution or phenotypic plasticity. More generally, these results show that threatened species introduced to restored habitats might lack adaptive potential and plasticity to adjust their phenology to their new environment. This constraint is also likely to limit their ability to face future challenges, including climate change.
Genome Resequencing of Laboratory Stocks of Burkholderia pseudomallei K96243

We have resequenced the genomes of four Burkholderia pseudomallei K96243 laboratory cultures and compared them to the reported genome sequence that was published in 2004. Compared with the reference genome, these laboratory cultures harbored up to 42 single-nucleotide variants and up to 11 indels, including a 31.7-kb deletion in one culture. ABSTRACT We have resequenced the genomes of four Burkholderia pseudomallei K96243 laboratory cultures and compared them to the reported genome sequence that was published in 2004. Compared with the reference genome, these laboratory cultures harbored up to 42 single-nucleotide variants and up to 11 indels, including a 31.7-kb deletion in one culture.
Postoperative Cognitive Dysfunction after Coronary Artery Bypass Grafting

Postoperative cognitive dysfunction is a common complication following cardiac surgery. The incidence of cognitive dysfunction is more pronounced in patients receiving a cardiac operation than in those undergoing a non-cardiac operation. Clinical observations demonstrated that pulsatile flow was superior to nonpulsatile flow, and membrane oxygenator was superior to bubble oxygenator in terms of postoperative cognitive status. Nevertheless, cognitive assessments in patients receiving an on-pump and off-pump coronary artery bypass surgery have yielded inconsistent results. The exact mechanisms of postoperative cognitive dysfunction following coronary artery bypass grafting remain uncertain. The dual effects, neuroprotective and neurotoxic, of anesthetics should be thoroughly investigated. The diagnosis should be based on a comprehensive cognitive evaluation with neuropsychiatric tests, cerebral biomarker inspections, and electroencephalographic examination. The management strategies for cognitive dysfunction can be preventive or therapeutic. The preventive strategies of modifying surgical facilities and techniques can be effective for preventing the development of postoperative cognitive dysfunction. Investigational therapies may offer novel strategies of treatments. Anesthetic preconditioning might be helpful for the improvement of this dysfunction.
Low-cost and Highly Sensitive Sensor for Determining Atorvastatin Using PbTe Nanoparticles-Modified Graphite Screen-Printed Electrode

1 Department of Chemistry, Shahid Bahonar University of Kerman, P.O. Box 76175-133, Kerman, Iran 2 Young Researchers Society, Shahid Bahonar University of Kerman, P.O. Box 76175-133, Kerman, Iran 3 Chemistry Department, Faculty of Science, Al‒Azhar University, Assiut, 71524, Egypt 4 Center of Excellence for Advanced Materials Research, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia E-mail: e.pourtaheri94@gmail.com (E. Pourtaheri), ma_taher@yaoo.com (M.A. Taher), vinodfcy@gmail.com (V.K. Gupta).
Complete Genome Sequence of Helicobacter pylori Strain GD63, Isolated from a Vietnamese Patient with a Gastric Ulcer

We present here the first complete genome sequence of Helicobacter pylori strain GD63, isolated from a 72-year-old male Vietnamese patient with a chronic gastric ulcer. The genome consists of a 1.6-Mbp chromosome and an 8.9-kbp plasmid. ABSTRACT We present here the first complete genome sequence of Helicobacter pylori strain GD63, isolated from a 72-year-old male Vietnamese patient with a chronic gastric ulcer. The genome consists of a 1.6-Mbp chromosome and an 8.9-kbp plasmid. The strain is cag pathogenicity island (cagPAI) and VacA positive and belongs to the hpEAsia lineage.
An interesting case of incidental solitary pulmonary nodule

A 54-year-old, nonsmoking woman was referred for a solitary pulmonary nodule (SPN) discovered during her routine preoperative pulmonary evaluation prior to right total knee replacement surgery. She had no respiratory symptoms. Around 4 months ago she had undergone a left total knee replacement surgery. She had a SPN at that time as well, but the radiologist erroneously reported it normal. So, she did not undergo any evaluation 4 months ago. She had diabetes mellitus and was on regular oral treatment. She denied prior history of antitubercular drug intake or any other chronic disease. There was no significant family history of respiratory disease or malignancy. Doubling time, clinical prediction models of malignancy and positive bronchus sign are useful in stepwise evaluation of SPN to avoid thoracotomy. GeneXpert can be used as initial diagnostic test for tuberculosis and detection of rifampicin resistance. http://ow.ly/N37030mB8Fi
Cryptic temporal changes in stock composition explain the decline of a flounder (Platichthys spp.) assemblage

Unobserved diversity, such as undetected genetic structure or the presence of cryptic species, is of concern for the conservation and management of global biodiversity in the face of threatening anthropogenic processes. For instance, unobserved diversity can lead to overestimation of maximum sustainable yields and therefore to overharvesting of the more vulnerable stock components within unrecognized mixed‐stock fisheries. We used DNA from archival (otolith) samples to reconstruct the temporal (1976–2011) genetic makeup of two mixed‐stock flounder fisheries in the Åland Sea (AS) and the Gulf of Finland (GoF). Both fisheries have hitherto been managed as a single stock of European flounders (Platichthys flesus), but were recently revealed to target two closely related species: the pelagic‐spawning P. flesus and the newly described, demersal‐spawning P. solemdali. While the AS and GoF fisheries were assumed to consist exclusively of P. solemdali, P. flesus dominated the GoF flounder assemblage (87% of total) in 1983, had disappeared (0%) by 1993, and remained in low proportions (10%–11%) thereafter. In the AS, P. solemdali dominated throughout the sampling period (>70%), and P. flesus remained in very low proportions after 1983. The disappearance of P. flesus from the GoF coincides in time with a dramatic (~60%) decline in commercial landings and worsening environmental conditions in P. flesus’ northernmost spawning ground, the Eastern Gotland Basin, in the preceding 4–6 years. These results are compatible with the hypothesis that P. flesus in the GoF is a sink population relying on larval subsidies from southern spawning grounds and the cause of their disappearance is a cessation of larval supply. Our results highlight the importance of uncovering unobserved genetic diversity and studying spatiotemporal changes in the relative contribution of different stock components, as well as the underlying environmental causes, to manage marine resources in the age of rapid anthropogenic change.
PIRSitePredict for protein functional site prediction using position-specific rules

Abstract Methods focused on predicting ‘global’ annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage. Methods to provide fine-grained ‘local’ annotation of functional sites (at the level of individual amino acid) are now coming to the forefront, especially in light of the rapid accumulation of genetic variant data. We have developed a computational method and workflow that predicts functional sites within proteins using position-specific conditional template annotation rules (namely PIR Site Rules or PIRSRs for short). Such rules are curated through review of known protein structural and other experimental data by structural biologists and are used to generate high-quality annotations for the UniProt Knowledgebase (UniProtKB) unreviewed section. To share the PIRSR functional site prediction method with the broader scientific community, we have streamlined our workflow and developed a stand-alone Java software package named PIRSitePredict. We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic transcriptomes of the following three cartilaginous fishes: Leucoraja erinacea (Little Skate), Scyliorhinus canicula (Small-spotted Catshark) and Callorhinchus milii (Elephant Shark). On average about 1200 lines of annotations were predicted for each species.
An update on the diagnosis and treatment of diabetic somatic and autonomic neuropathy

Diabetic peripheral neuropathy (DPN) is the most common chronic complication of diabetes. It poses a significant challenge for clinicians as it is often diagnosed late when patients present with advanced consequences such as foot ulceration. Autonomic neuropathy (AN) is also a frequent and under-diagnosed complication unless it is overtly symptomatic. Both somatic and autonomic neuropathy are associated with increased mortality. Multiple clinical trials have failed because of limited efficacy in advanced disease, inadequate trial duration, lack of effective surrogate end-points and a lack of deterioration in the placebo arm in clinical trials of DPN. Multifactorial risk factor reduction, targeting glycaemia, blood pressure and lipids can reduce the progression of DPN and AN. Treatment of painful DPN reduces painful symptoms by about 50% at best, but there is limited efficacy with any single agent. This reflects the complex aetiology of painful DPN and argues for improved clinical phenotyping with the use of targeted therapy, taking into account co-morbid conditions such as anxiety, depression and sleep disturbance.
Complete Genome Sequences of 12 B1 Cluster Mycobacteriophages, Gareth, JangoPhett, Kailash, MichaelPhcott, PhenghisKhan, Phleuron, Phergie, PhrankReynolds, PhrodoBaggins, Phunky, Vaticameos, and Virapocalypse

Twelve B1 cluster mycobacteriophages were isolated from soil samples collected in Philadelphia, PA, USA, using Mycobacterium smegmatis mc2 155 as a host, and were sequenced. The genome sequences range in size from 66,887 bp to 68,953 bp in length and have between 99 and 105 putative protein-coding genes. ABSTRACT Twelve B1 cluster mycobacteriophages were isolated from soil samples collected in Philadelphia, PA, USA, using Mycobacterium smegmatis mc2 155 as a host, and were sequenced. The genome sequences range in size from 66,887 bp to 68,953 bp in length and have between 99 and 105 putative protein-coding genes.
Intent-Based Real-Time 5G Cloud Service Provisioning

Software Defined Networking (SDN) and Network Function Virtualisation (NFV) have paved the way for programmability, flexibility and scalability of mobile networks. Both technologies offer significant advantages to the Network Operators (NOs) in terms of network management and service provisioning which widens their market to 3rd party providers such as Virtual Network Operators (VNOs) and Over-The-Top (OTT) Application Providers in domains such as Mobile BroadBand and Internet of Things (IoT). This paper, proposes an OTT Intent Based Network Framework for 5G Network Slice provisioning. The aim is to automate the task of network slicing through a declarative approach known as Intents while hiding network complexity from NOs, Mobile Infrastructure Tenants and VNOs. We provide an experimental validation of the Intent Framework with a scenario of a 5G IoT network slice deployment.
One-pot synthesis of soluble wholly aromatic liquid crystalline copoly(ester amide)s with high thermal and dimensional stability

Abstract Thermotropic liquid crystalline polymers (LCPs) have been of great interest for electronic packaging. Herein, we introduce a series of wholly aromatic, thermotropic LCPs from copoly(ester amide)s of 6-hydroxy-2-naphthalic acid, isophthalic acid, terephthalic acid, and 4-aminophenol, prepared by a convenient one-pot melt polycondensation. Almost synthesized copoly(ester amide)s exhibited good solubility in common organic solvents at room temperature. Furthermore, they possessed high thermal stability with 2% degradation temperatures (Tid) of 359–368 °C and the char yields (at 600 °C) of 50.3–55.6%. The synthesized copoly(ester amide)s had relatively low coefficient of thermal expansion (CTE) values, which were 35.85–41.21 ppm °C−1 in the temperature range of 50–200 °C. Furthermore, an annealing process could be employed to improve the thermomechanical properties of synthesized polymers. For instance, the CTE of sample LCP3 in range temperature of 275–315 °C was reduced by more than 90% after annealing at 320 °C for 1 h, implying the feasibility for electronic packaging.
Power Allocation in Downlink PDMA Systems

Pattern division multiple access (PDMA) is a multi- carrier non-orthogonal multiple access (NOMA), which can meet the requirements of massive user connections and super-high data rate in the fifth generation (5G) wireless networks. In this paper, we work on the optimization of power allocation to improve the performance of the downlink PDMA system significantly. Considering the perfect channel state information (CSI) is acquired at the transmitter, we propose an iterative power allocation (IPA) scheme based on the integration of the iterative subgradient method and the Mann iterative method. Moreover, Lagrange multipliers and the allocated power are updated until converged in each iteration. It is demonstrated in simulation results that the achievable sum throughput superiority of our proposed scheme over other schemes.
Optimizing Deep Learning Frameworks Incrementally to Get Linear Speedup: A Comparison Between IPoIB and RDMA Verbs

Deeper models and larger datasets are two major ingredients for applying deep learning (DL) on real-world problems, which inevitably shifts model training from on a single GPU card to on a GPU clusters due to limited GPU memory and time-to-solution requirements. High-speed low-latency RDMA-capable network fabrics like Infiniband and RoCE play an important role on coping with enoumous data exchanged during training. DL frameworks are built upon these fabrics with various APIs including IPoIB, MPI and RDMA Verbs. Tradeoffs are made between performance and usability when adapting DL frameworks onto RDMA-capable networks, which may result in high-performance yet hard-to-maintain and hard-to-merge code if improper design choices are made. This paper presents our approach to adapt MXNet, a modular versatile DL framework onto RDMA-capable networks. Dividing the training process on MXN et into P2P communication and A11Reduce commnunication, we add incremental optimizations on its message passing code. Experiments show that our approach exhibits near-linear speedups, whose parallel efficiency reaches 96% compared to 53% of the original IPoIB version when scaling to 100 GPU cards. In contrast to other MPI-based porting approach, our modifications are limited within MXNet's Parameter Server module, which is transparent for upper-layer operations, thus making no sacrifice on features like auto recovery and user-controlled consistency view.
Experimental and Modeling Framework for the Production of Cell and Protein-Based Biopharmaceutical Products

The advent of biological drugs has revolutionized the pharmaceutical industry by bringing to the market therapeutic agents capable of combining high potency with extremely high selectivity. Despite the financial success, this sector is constantly evolving to keep pace with the approval of an increasingly sophisticated catalogue of biotherapeutics. The present work aims at developing novel experimental and modeling strategies to optimize the production of cell and protein based biotherapeutics with tailored quality attributes. The first part of this thesis reports the development of two expansion processes to scale-up the cultivation of human pluripotent stem cells and T cells. Pluripotent stem cells can be expanded as floating aggregates in low-footprint suspension-based systems, but all currently reported processes rely on serial dissociation and reaggregation procedures to control the aggregate diameter below a critical size to maintain acceptable levels of pluripotency and cell viability. These procedures require the interruption of the culture and are usually associated with a reduced yield due to cell loss. This issue was solved through the development of a scalable bioreactor-based platform capable of maintaining a steady-state size distribution of stem cell aggregates through pulses of hydrodynamic shear stress, allowing the prolonged expansion of viable and phenotypically undifferentiated stem cells at high density. In the case of T cells, several studies have linked the clinical success rate of cell-based immunotherapies to the number of infused cells and to T cell-related attributes such as longevity, proliferative potential and metabolism. At the same time, most of the methods for T cell expansion in clinical trials are based on small-scale system in combination with medium formulations that aim at maximizing the growth rate of T cells at the expense of extensive differentiation in short-
Resource Allocation for Low-Latency Mobile Edge Computation Offloading in NOMA Networks

In this paper, we investigate the resource allocation for mobile edge computation offloading in non-orthogonal multiple access (NOMA) cellular networks. Leveraging NOMA, the massive connectivity can be supported to enable multiple cellular users to simultaneously upload their computation-intensive tasks on the same orthogonal resources, which improves spectral efficiency and reduces transmission delay. However, the co-channel interference in non- orthogonal spectrum sharing may potentially degrade the achievable rate of offloading computation tasks. Moreover, the overall delay of all cellular users in finishing computation offloading will increase if the computation resources at the edge server are not properly allocated. To minimize the maximum overall delay of all users, we formulate an optimization problem that jointly allocates communication resources and computation resources. Due to the non-convexity of the primal problem, we divide it into three subproblems. By exploiting their specific structures, an efficient algorithm is designed to obtain the suboptimal solution with low computational complexity. Simulation results are presented to demonstrate that our proposed algorithm can effectively reduce the overall delay of cellular users and fully exploit the benefit of NOMA on spectral efficiency, especially when the number of users is large.
Automating Data Preparation: Can We? Should We? Must We?

Obtaining value from data through analysis often requires significant prior effort on data preparation. Data preparation covers the discovery, selection, integration and cleaning of existing data sets into a form that is suitable for analysis. Data preparation, also known as data wrangling or extract transform load, is reported as taking 80% of the time of data scientists. How can this time be reduced? Can it be reduced by automation? There have been significant results on the automation of individual steps within the data wrangling process, and there are now a few proposals for end-to-end automation. This paper reviews the state-of-the-art, and asks the following questions: Can we automate data preparation – what techniques are already available? Should we – what data preparation activities seem likely to be able to be carried out better by software than by human experts? Must we – what data preparation challenges cannot realistically be carried out by manual approaches?