BRAND: a platform for closed-loop experiments with deep network models.

Objective.Artificial neural networks (ANNs) are state-of-the-art tools for modeling and decoding neural activity, but deploying them in closed-loop experiments with tight timing constraints is challenging due to their limited support in existing real-time frameworks. Researchers need a platform that fully supports high-level languages for running ANNs (e.g. Python and Julia) while maintaining support for languages that are critical for low-latency data acquisition and processing (e.g. C and C++).Approach.To address these needs, we introduce the Backend for Realtime Asynchronous Neural Decoding (BRAND). BRAND comprises Linux processes, termednodes, which communicate with each other in agraphvia streams of data. Its asynchronous design allows for acquisition, control, and analysis to be executed in parallel on streams of data that may operate at different timescales. BRAND uses Redis, an in-memory database, to send data between nodes, which enables fast inter-process communication and supports 54 different programming languages. Thus, developers can easily deploy existing ANN models in BRAND with minimal implementation changes.Main results.In our tests, BRAND achieved <600 microsecond latency between processes when sending large quantities of data (1024 channels of 30 kHz neural data in 1 ms chunks). BRAND runs a brain-computer interface with a recurrent neural network (RNN) decoder with less than 8 ms of latency from neural data input to decoder prediction. In a real-world demonstration of the system, participant T11 in the BrainGate2 clinical trial (ClinicalTrials.gov Identifier: NCT00912041) performed a standard cursor control task, in which 30 kHz signal processing, RNN decoding, task control, and graphics were all executed in BRAND. This system also supports real-time inference with complex latent variable models like Latent Factor Analysis via Dynamical Systems.Significance.By providing a framework that is fast, modular, and language-agnostic, BRAND lowers the barriers to integrating the latest tools in neuroscience and machine learning into closed-loop experiments.

BRAND: A platform for closed-loop experiments with deep network models.

Artificial neural networks (ANNs) are state-of-the-art tools for modeling and decoding neural activity, but deploying them in closed-loop experiments with tight timing constraints is challenging due to their limited support in existing real-time frameworks. Researchers need a platform that fully supports high-level languages for running ANNs (e.g., Python and Julia) while maintaining support for languages that are critical for low-latency data acquisition and processing (e.g., C and C++). To address these needs, we introduce the Backend for Realtime Asynchronous Neural Decoding (BRAND). BRAND comprises Linux processes, termed nodes , which communicate with each other in a graph via streams of data. Its asynchronous design allows for acquisition, control, and analysis to be executed in parallel on streams of data that may operate at different timescales. BRAND uses Redis to send data between nodes, which enables fast inter-process communication and supports 54 different programming languages. Thus, developers can easily deploy existing ANN models in BRAND with minimal implementation changes. In our tests, BRAND achieved <600 microsecond latency between processes when sending large quantities of data (1024 channels of 30 kHz neural data in 1-millisecond chunks). BRAND runs a brain-computer interface with a recurrent neural network (RNN) decoder with less than 8 milliseconds of latency from neural data input to decoder prediction. In a real-world demonstration of the system, participant T11 in the BrainGate2 clinical trial performed a standard cursor control task, in which 30 kHz signal processing, RNN decoding, task control, and graphics were all executed in BRAND. This system also supports real-time inference with complex latent variable models like Latent Factor Analysis via Dynamical Systems. By providing a framework that is fast, modular, and language-agnostic, BRAND lowers the barriers to integrating the latest tools in neuroscience and machine learning into closed-loop experiments.

Surface Modification of Pure Zinc by Acid Etching: Accelerating the Corrosion Rate and Enhancing Biocompatibility and Antibacterial Characteristics.

Zinc (Zn) has recently been identified as an auspicious biodegradable metal for medical implants and devices due to its tunable mechanical properties and good biocompatibility. However, the slow corrosion rate of Zn in a physiological environment does not meet the requirements for biodegradable implants, hindering its clinical translation. The present study aimed to accelerate the corrosion rate of pure Zn by utilizing acid etching to roughen the surface and increase the substrate surface area. The effects of acid etching on surface morphology, surface roughness, tensile properties, hardness, electrochemical corrosion and degradation behavior, cytocompatibility, direct cell attachment, and biofilm formation were investigated. Interestingly, acid-treated Zn showed an exceptionally high rate of corrosion (∼226-125 µm/year) compared to untreated Zn (∼62 µm/year), attributed to the increased surface roughness (Ra ∼ 1.12 µm) of acid-etched samples. Immersion tests in Hank's solution revealed that acid etching accelerated the degradation rate of Zn samples. In vitro, MC3T3-E1 cell lines in 50 and 25% conditioned media extracts of treated samples showed good cytocompatibility. Reduced bacterial adhesion, biofilm formation, and dispersion were observed for Staphylococci aureus biofilms cultured on acid-etched pure Zn substrates. These results suggest that the surface modification of biodegradable pure Zn metals by acid etching markedly increases the translation potential of zinc for various biomedical applications.

A study on transmission of Peste des petits ruminants virus between dromedary camels and small ruminants.

INTRODUCTION: In recent years Peste des petits ruminants (PPR) disease caused several epidemics in a wide range of susceptible hosts. The ability of the peste des petits ruminants virus (PPRV) to cross the species barrier necessitates further research, particularly on disease circulation and cross-species transmission between typical and atypical hosts to guide and facilitate the eradication program anticipated by the Food and Agriculture Organization (FAO) and the World Organization for Animal Health (OIE) in 2030. The aim of this study is to explore the role of dromedary camels as transmitters for PPR. METHODOLOGY: Four experiments were carried out on clinically healthy seronegative camels, sheep and goats. In experiment I, the animals were inoculated with a PPR- positive suspension of camel pneumonic lung homogenate. In the other three experiments either sheep and goats were inoculated and after three days were housed with camels or vice versa. RESULTS: Marked clinical signs suggestive of PPR were seen in sheep and goats while camels showed mild infection. Severe clinical signs of PPR were seen in sheep and goats when kept with inoculated camels. Postmortem examination revealed PPR lesions in all inoculated animals including camels. CONCLUSIONS: This study showed that dromedary camels infected with PPRV can transmit the disease to sheep and goats, even when they developed mild clinical signs.

In vivo performance of a rare earth free Mg-Zn-Ca alloy manufactured using twin roll casting for potential applications in the cranial and maxillofacial fixation devices.

A magnesium alloy containing essential, non-toxic, biodegradable elements such as Ca and Zn has been fabricated using a novel twin-roll casting process (TRC). Microstructure, mechanical properties, in vivo corrosion and biocompatibility have been assessed and compared to the properties of the rare earth (RE) element containing WE43 alloy. TRC Mg-0.5 wt% Zn- 0.5 wt% Ca exhibited fine grains with an average grain size ranging from 70 to 150 µm. Mechanical properties of a TRC Mg-0.5Zn-0.5Ca alloy showed an ultimate tensile strength of 220 MPa and ductility of 9.3%. The TRC Mg-0.5Zn-0.5Ca alloy showed a degradation rate of 0.51 ± 0.07 mm/y similar to that of the WE43 alloy (0.47 ± 0.09 mm/y) in the rat model after 1 week of implantation. By week 4 the biodegradation rates of both alloys studied were lowered and stabilized with fewer gas pockets around the implant. The histological analysis shows that both WE43 and TRC Mg-0.5Zn-0.5Ca alloy triggered comparable tissue healing responses at respective times of implantation. The presence of more organized scarring tissue around the TRC Mg-0.5Zn-0.5Ca alloys suggests that the biodegradation of the RE-free alloy may be more conducive to the tissue proliferation and remodelling process.

Does Aerobic Vaginitis Have Adverse Pregnancy Outcomes? Prospective Observational Study.

Background: Aerobic vaginitis (AV) is an aberration within the balanced vaginal microbiota. Only few reports have documented the adverse pregnancy outcomes related to AV. Nonetheless, the exact role of AV in pregnancy and the potential benefit of its screening need further study. Our goal was to evaluate the association between aerobic vaginitis (AV) in late pregnancy and maternal and neonatal outcomes. Methods: In this prospective observational study, a total of 600 singleton pregnant women with intact fetal membranes at a gestational age of 34-36 weeks were recruited (one hundred women with AV and 500 pregnant women without AV). The study protocol excluded patients with other forms of vaginal infection. Pregnancy outcomes were traced and documented. The primary outcome was the association between AV and preterm labor. The current study compared the maternal and neonatal outcomes among pregnant women with and without AV in unadjusted and adjusted analyses with the odds ratio (OR) and 95% confidence interval (CI) reported. Results: There was an association between AV and with preterm birth (adjusted OR 3.06, 95% CI 1.58-5.95) and prelabor rupture of membranes (adjusted OR 6.17, 95% CI 3.24-11.7). For neonatal outcomes, AV was associated with a higher incidence of neonatal ICU admission (adjusted OR 2.19, 95% CI 1.1-4.34). Severe forms of AV significantly increased the incidence of PTB (p = 0.0014) and PROM (p = 0.0094) when compared to less severe forms of AV. Conclusion: AV is common in late pregnancy and is linked to a diversity of adversative pregnancy outcomes including preterm birth, PROM, and neonatal ICU admission. Moreover, the incidence of PTB and PROM might further increase with the severity of AV. Clinicians should pay more consideration to vaginal microbiota assessment during pregnancy.

Effect of Na and Cooling Rate on the Activation of Mg-Ni Alloys for Hydrogen Storage.

In spite of favourable hydrogen storage properties such as low density, high theoretical capacity (7.6 wt% H/MgH2) and economics, commercial use of Mg-based alloys is not feasible due to long activation times, slow hydrogen sorption kinetics, and a high temperature for hydrogen release. Mg- Ni alloys have been considered promising materials for hydrogen storage systems as the Mg2Ni intermetallic phase enhances the kinetics of hydrogen absorption in Mg-Ni alloys through a catalytic effect. It has been suggested that the refinement of eutectic in Mg-Ni alloys can further improve hydrogen absorption kinetics and that this can be achieved through trace Na additions. However, the refinement of the eutectic can also be achieved by increasing the cooling rate during solidification. In this study we investigate the effect of cooling rate and Na additions to Mg-Ni alloys on hydrogen absorption kinetics. Our results indicate that Na additions improve the hydrogen absorption kinetics independent of eutectic refinement and that the effect of the latter is relatively small.

The Effect of Antenatal Vaginal Progesterone Administration on Uterine, Umbilical, and Fetal Middle Cerebral Artery Doppler Flow: A Cohort Study.

OBJECTIVE: This study aimed to evaluate the effect of vaginal progesterone (P) administration during the second and third trimesters of pregnancy on Doppler velocimetry of uterine, umbilical, and middle cerebral vessels. STUDY DESIGN: A prospective cohort study conducted on 80 women at risk for preterm labor. Uterine artery, umbilical artery, and middle cerebral artery (MCA) Doppler indices were measured before and after 1 week of administration of 200 mg twice daily vaginal P. The primary outcome parameter was the change of MCA pulsatility index (PI) after P administration. Secondary outcomes included changes in uterine artery and umbilical artery Doppler measurement. RESULTS: There was no significant changes of umbilical artery resistance index (RI) (0.69 ± 0.049 vs. 0.68 ± 0.041), umbilical artery PI (1.14 ± 0.118 vs. 1.11 ± 0.116), uterine artery RI (0.66 ± 0.12 vs. 0.66 ± 0.107), uterine artery PI (1.00 ± 0.26 vs. 1.016 ± 0.24), and MCA PI (1.27 ± 0.18 vs. 1.26 ± 0.23) measurements before and after 1 week of P administration, respectively. CONCLUSION: Administration of vaginal P has no significant effects on uterine artery, umbilical artery, and MCA Doppler indices.

The value of endocervical and endometrial lidocaine flushing before office hysteroscopy: A randomized controlled trial.

OBJECTIVE: To evaluate the safety and efficacy of flushing the cervical canal and the uterine cavity with local anesthetic in order to reduce the pain felt by patients during office hysteroscopy. METHODS: A double-blind randomized controlled trial was conducted between May 1, 2018, and February 28, 2019, involving 260 women undergoing office hysteroscopy at Kasr Al Ainy Hospital, Cairo, Egypt. Women were randomized using a computerized random number generator to intrauterine and intracervical instillation 5 minutes before the procedure of either 5 mL lidocaine 2% diluted in 15 mL normal saline, or 20 mL normal saline alone. The primary outcome measure was the visual analog scale (VAS) pain score reported by women during the procedure. Secondary outcomes included VAS score at 10 and 30 minutes after the procedure, the need for analgesia, and occurrence of vasovagal attacks. RESULTS: Women in the lidocaine flushing group reported a significantly lower VAS score during the procedure (1.8 ± 1.1 vs 5.2 ± 1.8) and 10 and 30 minutes after it (1.3 ± 1.15 and 0.8 ± 0.9 vs 4.3 ± 2.1 and 2.98 ± 1.96) when compared with control women (P<0.001). More women without lidocaine flushing experienced vasovagal attacks (25/130 vs 9/130, P<0.001) and needed analgesia (84/130 vs 13/130, P<0.001) when compared with women with lidocaine flushing. CONCLUSION: Flushing of the cervical canal and uterine cavity with local anesthetic significantly decreased pain sensation in women undergoing office hysteroscopy. CLINICALTRIALS.GOV: NCT03530488.

Perceptions, practices, and traditional beliefs related to neonatal jaundice among Egyptian mothers: A cross-sectional descriptive study.

Neonatal jaundice (NNJ) is one of the most common neonatal disorders worldwide. It is still a main cause of avoidable brain damage, physical and mental impairment, and probable death in newborns.We aimed to assess perceptions, practices, and traditional beliefs among Egyptian mothers toward NNJ that may contribute to delayed presentation and inappropriate management of hyperbilirubinemia.This descriptive, cross-sectional study was conducted from January to May 2015. We interviewed 400 Egyptian mothers who gave birth in <1 month before the study using a structured questionnaire. Participants were recruited from outpatients of Cairo University Teaching Hospital.This study revealed unexpected moderate knowledge and attitude scores of Egyptian mothers in most domains with a mean of 6.6 and 20.6, respectively, although the majority of them were illiterate or had low educational attainment. In terms of knowledge, 52.3% of participants had adequate knowledge about NNJ in the aspects of awareness, risk factors, management, and complications. Almost all participants exhibited moderate (89.8%) and high levels (10%) of positive attitudes toward NNJ. Maternal sociodemographic factors influenced knowledge level, attitudes, and behaviors related to NNJ in Egypt. Working mothers and those residing in urban areas were significantly more knowledgeable (P = 0.023 and 0.021, respectively), and attained higher attitude scores (P < 0.001 and P < 0.001, respectively) than housewives and rural ones. Moreover, significantly higher attitude scores (P < 0.001) were attained by those who had completed their university [22.3 (SD = 3.1)] or postgraduate education [22.2 (SD = 3.6)].The majority of Egyptian mothers have a satisfactory level of knowledge and attitudes related to NNJ. However, cultural beliefs and traditional infant care practices still have an impact on mothers regardless of their educational level.

Folic Acid Intake and Neural Tube Defects: Two Egyptian Centers Experience.

Neural tube defects (NTDs) are a group of congenital malformations with worldwide distribution and complex etiopathogenesis. Folic acid plays a pivotal role in their prevention. We aimed to identify the protective effect of folic acid intake against NTDs and its dependence on different socioeconomic and environmental factors in a cohort of mothers in Egypt. A cross-sectional study was carried over a period of 12 months on mothers who gave birth to babies with NTDs (group 1) and a control group with healthy offsprings (group 2). Both groups completed 2 questionnaires: food frequency questionnaire targeting the daily folate intake, and socioeconomic status and medical history questionnaire. Both groups of mothers received folate <800 µg/day, recommended for pregnant women. A strong association was detected between NTDs and urban residency with medium educated mothers, with negative consanguinity, who had folate intake < 400 µg daily, and who had their food long cooked. Each of these factors separately had a limited impact to cause NTDs, but when present together they did augment each other. Interestingly enough is the role of fava bean, cauliflower, spinach, and mango in predisposing of NTDs in the presence of the above-mentioned factors. The protective effect of folic acid intake against NTDs may depend on the synergism of different socioeconomic and environmental factors (which differ from country to another). In Egypt, females especially the medium-educated who live in urban areas should be well-informed with the value of folate intake in the periconceptional period.

Peste des petits ruminants outbreaks in White Nile State, Sudan.

Eight outbreaks of peste des petits ruminants in sheep and goats were reported in White Nile State, Sudan, between 2008 and 2009. A mortality rate of 4.2% was reported across the different outbreaks. Clinically the disease was characterised by high fever, ocular and nasal discharge, pneumonia, ulceration of the mucous membranes, diarrhoea and death. The postmortem findings included necrotic lesions in the mouth and gastrointestinal tract, and swollen, oedematous lymph nodes associated with the lungs and intestine. Of the 209 serum samples tested by competitive enzyme-linked immunosorbent assay, 113 (54%) were found positive. Peste des petits ruminants virus was confirmed in tissues, nasal swabs and blood samples by immunocapture enzyme-linked immunosorbent assay, reverse-transcription polymerase chain reaction and isolation of the virus in culture of lamb testicle cells.

Phylogenetic analysis of eight sudanese camel contagious ecthyma viruses based on B2L gene sequence.

BACKGROUND: Camel contagious ecthyma (CCE) is an important viral disease of camelids caused by a poxvirus of the genus parapoxvirus (PPV) of the family Poxviridae. The disease has been reported in west and east of the Sudan causing economical losses. However, the PPVs that cause the disease in camels of the Sudan have not yet subjected to genetic characterization. At present, the PPV that cause CCE cannot be properly classified because only few isolates that have been genetically analyzed. METHODS AND RESULTS: PCR was used to amplify the B2L gene of the PPV directly from clinical specimens collected from dromedary camels affected with contagious ecthyma in the Sudan between 1993 and 2013. PCR products were sequenced and subjected to genetic analysis. The results provided evidence for close relationships and genetic variation of the camel PPV (CPPV) represented by the circulation of both Pseudocowpox virus (PCPV) and Orf virus (ORFV) strains among dromedary camels in the Sudan. Based on the B2L gene sequence the available CPPV isolates can be divided into two genetic clades or lineages; the Asian lineage represented by isolates from Saudi Arabia, Bahrain and India and the African lineage comprising isolates from the Sudan. CONCLUSION: The camel parapoxvirus is genetically diverse involving predominantly viruses close to PCPV in addition to ORFVs, and can be divided into two genetically distant lineages. Based on sequences of the B2L gene it is not possible to suggest that the viruses that cause CCE form a monophylogenetic group or species within the PPV phylogeny.

Mixed infection of peste des petits ruminants virus (PPRV) and other respiratory viruses in dromedary camels in Sudan, an abattoir study.

This study was intended to determine the role played by peste des petits ruminants (PPR) in causing respiratory infections in camels and its association with other respiratory viruses. A total of 474 lung specimens showing pneumonia were collected from clinically healthy camels in slaughterhouses at five different areas in Sudan. Using immunocapture ELISA (IcELISA), 214 specimens (45.1 %) were found to be positive for PPR antigen. The highest prevalence was found in central Sudan (59.9 %) then northern Sudan (56.6 %) and eastern Sudan (26.6 %). Parainfluenza virus 3 (PIV 3), respiratory syncytial virus (RSV), bovine herpes virus-1 (BHV-1), bovine viral diarrhea (BVD), and adenovirus were detected in 4.4, 2.9, 2.0, 9.0, and 1.3 % of the specimens, respectively. PPR antigen was found in about 50 % of specimens that showed positive result for other viral antigens. Twenty-five of 28 BVD, 15 of 16 PIV3, 8 of 12 RSV, 4 of 4 adenovirus, and 4 of 5 BHV-1 were found in association with other respiratory antigens. Results revealed the existence of PPRV infection in dromedary camels in Sudan and present evidence for mixed virus infection, suggesting that respiratory infections in camels might be exacerbated by PPRV.

Imaging of thoracic aortic injury.

Isthmic aortic rupture or disruption should be systematically sought when there is high kinetic energy trauma to the thorax. This condition is extremely serious and life threatening. It needs to be diagnosed rapidly but diagnostic pitfalls must be avoided. CT angiography is the standard examination. The main CT signs of rupture or disruption of the thoracic aorta are periaortic hematoma, intimal flap, pseudo-aneurysm and contrast agent extravasation. There are three types of lesion: intimal, subadventitial or pseudo-aneurysmal, and complete rupture with lesion of the three tunicae, and it is important to grade them for better therapeutic management. The main diagnostic pitfalls of the CT scan are the presence of a ductus diverticulum and post-isthmic fusiform dilatation. Associated lesions must not be overlooked. The most common are ruptures of the aortic root and the thoracic aorta in the diaphragmatic hiatus.

Novel NSP1 genotype characterised in an African camel G8P[11] rotavirus strain.

Animal-human interspecies transmission is thought to play a significant role in influencing rotavirus strain diversity in humans. Proving this concept requires a better understanding of the complete genetic constellation of rotaviruses circulating in various animal species. However, very few whole genomes of animal rotaviruses, especially in developing countries, are available. In this study, complete genetic configuration of the first African camel rotavirus strain (RVA/Camel-wt/SDN/MRC-DPRU447/2002/G8P[11]) was assigned a unique G8-P[11]-I2-R2-C2-M2-A18-N2-T6-E2-H3 genotype constellation that has not been reported in other ruminants. It contained a novel NSP1 genotype (genotype A18). The evolutionary dynamics of the genome segments of strain MRC-DPRU447 were rather complex compared to those found in other camelids. Its genome segments 1, 3, 7-10 were closely related (>93% nucleotide identity) to those of human-animal reassortant strains like RVA/Human-tc/ITA/PA169/1988/G6P[14] and RVA/Human-wt/HUN/Hun5/1997/G6P[14], segments 4, 6 and 11 shared common ancestry (>95% nucleotide identity) with bovine rotaviruses like strains RVA/Cow-wt/CHN/DQ-75/2008/G10P[11] and RVA/Cow-wt/KOR/KJ19-2/XXXX/G6P[7], whereas segment 2 was closely related (94% nucleotide identity) to guanaco rotavirus strain RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1]. Its genetic backbone consisted of DS-1-like, AU-1-like, artiodactyl-like and a novel A18 genotype. This suggests that strain MRC-DPRU447 potentially emerged through multiple reassortment events between several mammalian rotaviruses of at least two genogroups or simply strain MRC-DPRU447 display a unique progenitor genotypes. Close relationship between some of the genome segments of strain MRC-DPRU447 to human rotaviruses suggests previous occurrence of reassortment processes combined with interspecies transmission between humans and camels. The whole genome data for strain MRC-DPRU447 adds to the much needed animal rotavirus data from Africa which is limited at the moment.

Asian lineage of peste des petits ruminants virus, Africa.

Interest in peste des petits ruminants virus (PPRV) has been stimulated by recent changes in its host and geographic distribution. For this study, biological specimens were collected from camels, sheep, and goats clinically suspected of having PPRV infection in Sudan during 2000-2009 and from sheep soon after the first reported outbreaks in Morocco in 2008. Reverse transcription PCR analysis confirmed the wide distribution of PPRV throughout Sudan and spread of the virus in Morocco. Molecular typing of 32 samples positive for PPRV provided strong evidence of the introduction and broad spread of Asian lineage IV. This lineage was defined further by 2 subclusters; one consisted of camel and goat isolates and some of the sheep isolates, while the other contained only sheep isolates, a finding with suggests a genetic bias according to the host. This study provides evidence of the recent spread of PPRV lineage IV in Africa.

An outbreak of peste des petits ruminants (PPR) in camels in the Sudan.

In mid-August 2004, an outbreak of a previously unknown fatal disease of camels was reported to Kassala State veterinary authorities. Several areas in the state were visited during August-October 2004 to collect epidemiological data and specimens for diagnosis. Clinically the disease was characterized by sudden death of apparently healthy animals and yellowish and later bloody diarrhea and abortion. The disease outbreaks coincided with the seasonal movement of animals towards autumn green pasture. Death was always sudden and proceeded with colic and difficulty in respiration. Mortality rate ranged between 0% and 50% and vary in accordance with the area with a mean of 7.4%. More than 80% of deaths were in pregnant and recently-delivered she-camels. All age, sex and breed groups were affected but more than 50% of deaths were reported in adult animals in comparison to calves and young camels. The main post-mortem findings include lung congestion and consolidation, paleness and fragility of liver, enlarged lymph nodes and congestion and hemorrhage of small intestine and stomach. Agar gel diffusion test (AGDT), RT-PCR and virus isolation in cell culture gave positive results for peste des petits ruminants virus (PPRV), a virus belonging to the Morbillivirus, Genus, member of the family Paramyxoviridae. The effect of this new devastating disease on camel production in the affected area was discussed as well as proposals for future research.