bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the levels of lead and cadmium in canned fish and meat, imported to the local markets of Diyala Province, Iraq
Authors: Hussein S.A. , Rathi M.H. , Kadhim T.J.
Published: June 2021

Food of animal origin is among those products that provide many important nutrients. The food industry employs numerous technologies which allow manufacturing of products with diversified shelf life. The objective of the study was to determine the contents of lead (Pb) and cadmium (Cd) in 49 samples of canned fish and meat from different brands by using the flame atomic absorption spectroscopy (FAAS).It was found that the highest mean of lead in canned fish was 0.2294 ± 0.00014mg/kg, while the lowest mean was 0.0214 ± 0.00049mg/kg, the highest mean of cadmium in canned fish was 0.2322 ± 0.00686 mg/kg and the lowest was 0.1170 ± 0.00021 mg/kg. The highest mean of lead in chicken and beef meat and was 0.2454±0.03486 mg/kg, while the lowest mean was 0.0217 ± 0.00057 mg/kg. For cadmium, the highest mean in chicken and beef meats was 0.3091 ± 0.00014 mg/kg and the lowest was 0.1214 ± 0.00021 mg/kg. The statistical analysis showed that there were significant differences (p≤0.05) between the studied samples for each element. Lead values in the tested samples varied between values above the acceptable limits recommended by the WHO or within the global limits, while the cadmium values for all tested samples exceeded the acceptable limits adopted by the WHO.
Molecular detection of Quinolone Resistant-Salmonella isolates from poultry farms in Al- kut, IRAQ.
Authors: Al-Safi Zaid Hasan
Published: June 2021

The current study included collecting clocae samples from poultry within Wasit Governorate’s farms. It aimed to isolate salmonella from broiler chickens and to determine the pattern of resistance to antimicrobial drug besides to detect of Quinolone Resistance genes. The results showed isolation of (3) types of Salmonella (s. gallinarum s.typhimurium, s.enteritidis). The highest percentage of resistance isolates to tested antibiotics (nalidixic acid, ciprofloxacin ofloxacin, enrofloxacin, levofloxacin) depending on disc diffusion test, were as follow (81%), (78.26) and (91.66%)respectively. The remaining small percentage of the isolates were sensitive to all quinolones. On the other hand, The results of the molecular diagnostics that were conducted found that all antibiotic-resistant strains contain qnr B and iaa (6) ib gene.
Soil Properties and Influencing in citrus Agriculture in Husseinieh district
Authors: Al-Taei Alaa J , Al-Zamili Ayed J
Published: June 2021

Soils different in the study area accordingly on its location change, as the natural ingredients lead Such In determining the characteristics of it soils and drawing their features and the possibility of using them in various agricultural activities, The search included a study and analysis of the physical and chemical characteristics of soil in Al-Husayniyah district, northeast of Karbala Governorate, by (24) samples and for (12) sites. To know the changes in its physical properties represented in soil texture, soil moisture and temperature, as for its chemical properties, it was represented by SOM, pH and EC. Results of the search showed that the physical and chemical properties of the soil of the study area are suitable for Agriculture citrus fruits, the soil was characterized by a texture that ranged from Sand Loamy and Sandy loam and sandy, which made it good and the movement of air and water was relatively more good, allowing the roots of plants to penetrate through it, In addition to soil moisture, moderate temperature and low salinity their rates are less than 4 dS.m-1 as such, it is considered a low-salinity soil, which encouraged the prosperity of cultivating citrus trees in the Al-Husseiniya district.
Kinetic Study of removal Zinc Oxide Nanoparticles from Aqueous Solutions on synthesized CH-g-P(AAc-co-Am)
Authors: Hussain Namer A. , Jasim Layth S.
Published: June 2021

The research contains the preparation of Cross-linking Hydrogel (Chitosan-g-poly (AA – Co – Am)). The way polymerization of the free radicals via utilizing the potassium persulfate as the initiator for the reaction, too with N, N’-methylene bis-acrylamide (NMBA)as a cross-linking agent The mixture gets treated via Acrylamide that includes The adsorption time was 120 mint. The adsorption was proved via utilizing the FESEM and FTIR analysis and analysis TEM And knowing the surface roughness AFM. Also, TGA appears that the hydrogel is stable at high temperatures. The kinetics parameter Study of the Hydrogel was performed via utilizing the Zinc oxide applies to the adsorption from the Pseudo-second order model Because (R2) an approximation of the correct one.
Suitability of Groundwater in Al-Qaim Area/West of Iraq for different life uses
Authors: Alsalmani Mohamed H. , Al-Shama’a Aysser M.
Published: June 2021

A total of twenty wells were studied in Al-Qaim region in the western part of Iraq. The main purpose of the present study was to investigate, evaluate and specify adequacy of the hydrochemistry properties of groundwater and its suitability for different uses. The studied area is located between latitude (34 16 52 5-34 21 56 41 1 15 -41 8 16.5) east. The obtained results are gain through a constant procedure started from field tours as a first step and ending with recorded results from laboratory analysis. The results explained the changing between dry and wet periods which provide a noticeable increasing for dry analysis comparing with wet one. Physical properties which include pH, Temperature, Electrical Conductivity and TDS were computed to show increasing in dry period by (12.78, 5.01, 7.34 and 14.27) % for T, pH, TDS and EC respectively. On the other hand, chemical properties which include cations (Ca2+, Na+, Mg2+ and K+) and anions (Cl−, SO4
2- and HCO3
−) were calculated to show increasing in dry period by (6.40, 7.87, 13.03 and 16.32) % for (Ca2+, Na+, Mg2+ and K+) respectively and (5.30, 4.28 and 5.74) for (Cl−, SO4
2- and HCO3
−) respectively. From obtained results, it is worth mentioning that the groundwater in the studied area is adequate for livestock, building, agricultural and irrigation purposes and not adequate for drinking and industrial purposes.
Effect of Cu doping ZrO2Thin films on physical properties grown by spray pyrolysis deposition
Authors: Habubi Nadir F , Abdulmunem Oday M , Shaban Zina M , Agool Ibrahim R , Dawood Mohammed O , Chiad Sami S
Published: June 2021

Zirconium oxide (ZrO2) and Cu doped ZrO2films were grown successfully by spray pyrolysis deposition (SPD). The structural, surface morphology and optical properties were analyzed. XRD patterns reveal films polycrystallinity and monoclinic phase intensity of ZrO2with preferred orientation along M (111) plane increasing with increasing doping. The grain size was found to increase from 25 nm to 29.83 nm with increase in Cu doping. AFM images assure that films were nanostructure and the surface morphology and roughness depend on doping concentration. The optical bandgap energy decreases from 3.2 to 2.6 eV with increasing doping concentration.
Synthesis, Characterization and H2S Gas Sensor Performance of Hydrothermal Prepared SnO2 Films Nanostructures
Authors: Shano Ahmed M , Khudhur Ahmed Mahmood , Hassan Abbas Abdul Salam , Bakr Nabeel A. , Ali Iftikhar M.
Published: June 2021

In this work, tin oxide thin films were successfully synthesized by hydrothermal method and depositing on silicon substrates by spin coating technique at room temperature with thickness of about 325±5 nm. The structural, surface morphological, optical and gas sensor properties have been investigated. The XRD results showed that SnO2 films are polycrystalline in nature with tetragonal. The FESEM images of SnO2 clearly indicate that the oxide possesses has like cauliflower like shapes. The optical properties show that the optical energy gap follows allowed direct electronic transition calculated using Tauc’s equation. The H2S toxic gas sensing properties of SnO2 thin film are examined as a function of time and operating temperature. High sensitivity (197%) was attained at operating temperature of 200 °C with fast response and recovery times.
Effect of welding speed on mechanical properties and corrosion resistance rates of filler induced friction stir welded AA6082 and AA5052 joints
Authors: Sasikumar A , Gopi S , G Mohan Dhanesh
Published: June 2021

Friction Stir Welding (FSW) was carried out to examine the influence of filler materials and varying process parameters on the microhardness and the joints corrosion resistance properties. Aluminium alloys 6082 and 5052, having 8 mm thickness was joined by varying parameters. The primary process parameters are rotational speed, tool travel speed, plunge depth, filler holes centre distance and filler ratio. The hardness at the weld nugget zone and corrosion rate evaluations were analyzed. The best results were obtained for the parameter combinations of 1150 rpm tool rotation, 130 mm min−1 tool travel, 0.2 mm tool plunge, the filler holes centre distance 2 mm and a powder filler made of 95% magnesium and 5% chromium.
Recent regime of persistent hypoxia in the Baltic Sea
Authors: Kõuts Mariliis , Maljutenko Ilja , Elken Jüri , Liu Ye , Hansson Martin , Viktorsson Lena , Raudsepp Urmas
Published: June 2021

Oxygen deficiency, in the form of hypoxia and anoxia, is a direct consequence of the eutrophication of the Baltic Sea. There is ongoing debate concerning the increasing extent of hypoxia. We analyse the integral metrics of hypoxia and anoxia: (1) temporal evolution of the hypoxic and anoxic area and volume, (2) the spatial distribution of the probabilities of hypoxia and anoxia occurrence in the Baltic Sea. The results are based on the state-of-the-art coupled physical and biogeochemical numerical model reanalysis data from Copernicus Marine Environment Monitoring Service for the period of 1993–2017. Statistical analysis showed that the variability of hypoxic and anoxic areas since the year 2000 represents stationary processes around their respective mean levels. From 2000 to 2017, the hypoxic area varies between 50000 and 80000 km2 and the anoxic area varies between 10000 and 50000 km2. Different methods and data sources indicate that the uncertainties of the estimates account for about 10000 km2. We suggest that the loss of stationarity of the time series of the hypoxic area would be an indication of the regime change of hypoxia development in the Baltic Sea. Probability distribution maps of hypoxia and anoxia provide detailed information about the persistency of hypoxia and anoxia in different parts of the Baltic Sea. The probability of hypoxia exceeds 0.9 in the eastern and western Gotland basins and in the deep area of the Bornholm basin. The Gulf of Finland and the shallower areas that connect different deep basins of the Baltic Sea exhibit seasonal and episodic hypoxia. The 80 m and 120 m isobaths are the approximate bathymetry limits of hypoxia and anoxia occurrence, respectively. Our study supports previous knowledge that hypoxia development is controlled to a large degree by the depth of the permanent halocline.
Monolithically integrated electro-optic modulator fabricated on lithium niobate on insulator by photolithography assisted chemo-mechanical etching
Authors: Liang Youting , Zhou Junxia , Yin Difeng , Zheng Yong , Qi Hongxin , Wang Min , Fang Zhiwei , Wu Rongbo , Cheng Ya
Published: June 2021

Integrated electro-optic (EO) modulators are one of the building blocks of photonic integrated circuits. Here, we design and fabricate an EO Mach–Zehnder waveguide modulator on lithium niobate on insulator using photolithography assisted chemo-mechanical etching technology. We optimize the performance of multi-mode interferometer which serves as the 3 dB splitter as well as that of the inverse taper to achieve efficient fiber-waveguide coupling, resulting in a fiber-to-fiber insert loss of 7.6 dB for the fabricated device, with a half wave voltage (HWV) (Vπ
) of 0.84 V and a HWV-length product (Vπ
× L) of 3.4 V cm. The all-optical-lithography fabrication approach holds the promising potential for mass production of EO modulators of cost-effectiveness and low Vπ
.
Do bovids evolve hindquarter markings for anti-predation?
Authors: Yu Cong , Chen Lixin , Ning Sihan , Ullah Sana , Li Zhongqiu
Published: June 2021

Conspicuous coloration in animals serves many functions such as anti-predation. Anti-predation strategies include motion dazzle and flash behavior. Motion dazzle markings can reduce the probability of being preyed on because the predators misjudge their movement. In flash behavior, prey demonstrate conspicuous cue while fleeing; the predators follow them; however, the prey hide their markings and the predators assume that the prey has vanished. To investigate whether bovids use conspicuous hindquarter markings as an anti-predatory behavior, we undertook phylogenetically controlled analyses to explore under what physiological characteristics and environmental factors bovids might have this color pattern. The results suggested that rump patches and tail markings were more prevalent in bovids living in larger-sized groups, which supports the hypothesis of intraspecific communication. Moreover, we observed the occurrence of conspicuous white hindquarter markings in bovids having smaller body size and living in larger groups, suggesting a motion dazzle function. However, the feature of facultative exposing color patterns (flash markings) was not associated with body size, which was inconsistent with predictions and implied that bovids may not adopt this as an anti-predator strategy. It was concluded that species in bovids with conspicuous white hindquarter markings adopt motion dazzle as an anti-predation strategy while fleeing and escaping from being prey on.
To be or not to be a target: that is the question to manage mixed fisheries
Authors: Garcia Dorleta , Arostegui Inmaculada , Prellezo Raúl
Published: June 2021

Simulation models are used extensively to evaluate the performance of fisheries management strategies, though they must be validated to ensure that they accurately represent the real system. One of the quantitative methods available to advance in the process of validating simulation models is global sensitivity analysis (GSA). However, its use in fisheries management has been very limited. When GSA is applied to management strategy evaluation implementations, it can also help manage available resources efficiently with respect to uncertainty in the management process and the conditioning of simulation models. Mixed-fisheries management plans were recently implemented for demersal fisheries in the Northeast Atlantic, which were evaluated previously using complex bioeconomic models. Here, we applied GSA to the model used in Iberian waters, employing an efficient model design to introduce uncertainty in every single input factor. While most biological factors contributed significantly to the variance of results, only few economic factors did. Moreover, we found that increasing accuracy in the stock assessment process would mainly impact management advice and that only the management of target stocks had a real impact on the system. This highlights the importance of properly managing hake (Merluccius merluccius), which is currently managed using an empirical harvest control rule.
Political Subjectivation and the In/Visible Politics of Migrant Youth Organizing in Germany and the United States
Authors: Schwiertz Helge
Published: June 2021

In countries of the Global North, migrant youth with a precarious legal status are not commonly seen as political subjects, but as subjects of politics. Against this background, this paper reflects on how migrant youth nevertheless manage to organize themselves and intervene in the dominant society, thereby emerging as unforeseen political subjects. Discussing acts of citizenship and autonomy of migration approaches, I argue for the use of a multifaceted concept of collective political subjectivation. Doing so sheds light on how migrant struggles exceed categorization as protest, moments of rupture, or imperceptible subversion. While drawing on Jacques Rancière's concept of “political subjectivation,” I go beyond his rather narrow focus by highlighting aspects of democracy, transgression, and in/visibility, as well as creative modes of identity-making, which could be further developed in the literature on political subjectivities and migrant struggles. This theoretical reflection builds on two qualitative case studies on migrant youth organizing in Germany and the United States that show the relevance of visible as well as relatively invisible politics. In both cases, I analyze two events that provide insight into this complex notion of political subjectivation: “Coming Out of the Shadows” in the United States and the counter-conferences in Germany.
Hypoplasia of abdominal wall muscles following massive fetal persistent chylous ascites without anemia
Authors: Yamaguchi Tetsu , Tamaru Shunsuke , Takano Natsuko , Sato Kazuko , Sakurai Hayato , Ohashi Hirofumi , Kamei Yoshimasa
Published: June 2021

Abdominal wall hypoplasia is a widely known clinical finding of genetic disorders such as the prune belly syndrome. On the other hand, there are few cases of abdominal wall muscle hypoplasia associated with fetal ascites due to fetal hydrops caused by fetal anemia have been reported. We report a case of fetal chylous ascites without anemia, resulting in abdominal wall muscle hypoplasia and flabby skin. At 17 weeks of gestation, fetal ascites was first detected and deteriorated without anemia. At 28, 33 and 36 weeks of gestation, paracentesis was performed three times because of cardiovascular impairment, confirming chylous ascites. After birth, the baby exhibited a flabby skin and lateral abdominal wall hypoplasia, resulting in difficulties in maintaining a sitting posture at 10 months of age. The genetic test using the TruSight One Sequencing Panels found no genetic variants. This case suggests that abdominal wall hypoplasia could be associated with fetal ascites without anemia.
John Davenant and the English Appropriation of the Synod of Dort
Authors: Hampton Stephen
Published: June 2021

Chapter 2 builds on the previous chapter’s emphasis on the breadth and pastoral orientation of the Reformed Conformist approach to grace, with an examination of the Collegiate Suffrage of the British delegates at the Synod of Dort (1618–19). It underlines that the Suffrage was drawn up to make room for Davenant and Ward’s distinctive reading of the death of Christ, a reading shared by influential clerics at home. The chapter then shows how the positions adopted in the Suffrage were echoed but also given a different inflection in the lectures that Davenant delivered in Cambridge when he returned from the Synod. Davenant’s lectures on predestination and the death of Christ show how he adapted the teaching of Dort to suit his own reading of the Church of England’s confessional position, whilst offering extensive advice on its pastoral application both in the pulpit and in the spiritual lives of the faithful.
Philosophical Background
Authors: Timmons Mark
Published: June 2021

This chapter provides a brief overview of certain elements of Kant’s metaphysics and epistemology that are essential background for understanding certain features of his ethical theory. In particular, it presents Kant’s distinction between the ‘world of sense’ or ‘phenomenal world’ and the ‘world of understanding’ or ‘noumenal world’ as a basis for explaining the limits of theoretical cognition which rules out theoretical cognition and knowledge of God, immortality of the soul, and freedom of the will, yet allows Kant to affirm their reality on moral grounds, needed to explain how the highest good is possible. Of importance for understanding certain claims in his work on virtue is the distinction between the phenomenal world and the noumenal world as it applies to human beings. The chapter concludes with reflections on the relation between Kant’s ethics and his metaphysical and epistemological commitments.
The Theory and Practice of Mediation: A Reply to Professor Susskind
Authors: Stulberg Joseph B.
Published: June 2021

This article details the theory and practice of mediation. The mediation process can be characterized as follows: it is (1) a noncompulsory procedure in which (2) an impartial, neutral party is invited or accepted by (3) parties to a dispute to help them (4) identify issues of mutual concern and (5) design solutions to these issues, (6) which are acceptable to the parties. The mediator’s role is to convey each party’s proposals in a language that is both faithful to the desired objectives of the party and formulated to ensure the highest degree of receptivity by the listener. The article then looks at the profile of a mediator and explores mediator strategies for building a settlement. It also considers environmental dispute mediation.
Fermion masses and mixings in a U(1)X model based on the Σ(18) discrete symmetry
Authors: Vien V V , Hernández A E Cárcamo , Long H N
Published: June 2021

We have built a renormalizable $U(1)_X$ model with a $\Sigma (18)\times Z_4$ symmetry, whose spontaneous breaking yields the observed standard model (SM) fermion masses and fermionic mixing parameters. The tiny masses of the light active neutrinos are produced by the type I seesaw mechanism mediated by very heavy right-handed Majorana neutrinos. To the best of our knowledge, this model is the first implementation of the $\Sigma (18)$ flavor symmetry in a renormalizable $U(1)_X$ model. Our model allows a successful fit for the SM fermion masses, fermionic mixing angles, and CP phases for both quark and lepton sectors. The obtained values for the physical observables of both quark and lepton sectors are in accordance with the experimental data. We obtain an effective neutrino mass parameter of $\langle m_{ee}\rangle=1.51\times 10^{-3}\, \mathrm{eV}$ for normal ordering (NO) and $\langle m_{ee}\rangle =4.88\times 10^{-2} \, \mathrm{eV}$ for inverted ordering (IO), which are well consistent with the recent experimental limits on neutrinoless double beta decay.
Rhizosphere Microbes Influence Host Circadian Clock Function
Authors: Hubbard Charley J. , McMinn Robby , Weinig Cynthia
Published: June 2021

The circadian clock is an important determinant of fitness that is entrained by local conditions. Aside from abiotic factors, individual pathogenic soil bacteria affect circadian clock function in plant hosts. Yet, in nature, plants interact with diverse microbial communities, and the effect of complex communities on clock function remains unclear. In Arabidopsis thaliana and its wild relative, Boechera stricta, we used diverse rhizosphere inoculates and host genotypes to test the effect of complex rhizosphere microbial communities on the host circadian clock. A. thaliana plants with an intact rhizosphere microbiome expressed a circadian period closer to 24 h in duration and significantly shorter (by 48 min on average) relative to plants grown with a disrupted microbiome. Wild-type host genotypes of A. thaliana differed in clock sensitivity to microbes, with one genotype (Landsberg erecta) expressing a 119-min difference in circadian period length across rhizosphere microbial treatments. A similar pattern of clock sensitivity to soil microbes was observed in B. stricta. Finally, rhizosphere microbes collected from the mutant genotype toc1-21 of A. thaliana with a short-period phenotype and used as inoculate significantly shortened the long-period phenotype of the clock mutant genotype ztl-1. The results indicate that complex rhizosphere microbial communities affect host clock function.
Ultrasound-Guided Distal Forearm Fracture Reduction by Pediatric Emergency Physicians
Authors: Scheier Eric , Balla Uri
Published: June 2021

Introduction

Fracture reduction under point-of-care ultrasound (POCUS) guidance facilitates measurement of residual angulation or displacement that may not be apparent on examination. Point-of-care ultrasound is without patient or staff exposure to ionizing radiation and enlists no additional staffing resources or patient transfer.

Methods

We conducted a chart review of all children who underwent reduction of a distal forearm fracture in the pediatric emergency department over a 2-year period, from September 2018 to September 2020. We compared length of stay (LOS) with that for orthopedist-performed distal forearm reductions during the study period. We allowed a 6-week lag period to ensure no missed rereduction before analyzing the data. After reduction, children were instructed to follow up with an orthopedist within 1 week. Children with loss of reduction on orthopedic follow-up are referred back through our emergency department for operative reduction.

Results

A total of 74 children with 75 distal forearm fractures were identified. Average LOS was 179 minutes for the pediatric emergency medicine physician reductions and 215 minutes for the orthopedist reductions (P < 0.001). Ninety-six percent of reductions were completed with POCUS assistance, and 61% had less than 5 degrees of angulation on postreduction radiography. Only 2.7% of children underwent rereduction.

Conclusions

Distal forearm fracture reductions by a pediatric emergency medicine physician under POCUS guidance have a high rate of excellent alignment, low rate of failed reduction, and significantly shorter LOS (P < 0.001) than reductions performed by orthopedists.
Perfusate Enzymes and Platelets Indicate Early Allograft Dysfunction After Transplantation of Normothermically Preserved Livers
Authors: Weissenbacher Annemarie , Bogensperger Christina , Oberhuber Rupert , Meszaros Andras , Gasteiger Silvia , Ulmer Hanno , Berchtold Valeria , Krendl Felix J. , Fodor Margot , Messner Franka , Hautz Theresa , Otarashvili Giorgi , Resch Thomas , Margreiter Christian , Maglione Manuel , Irsara Christian , Griesmacher Andrea , Raynaud Marc , Breitkopf Robert , Troppmair Jakob , Öfner Dietmar , Cardini Benno , Schneeberger Stefan
Published: June 2021

Background.

Normothermic machine perfusion (NMP) has become a clinically established tool to preserve livers in a near-physiological environment. However, little is known about the predictive value of perfusate parameters toward the outcomes after transplantation.

Methods.

Fifty-five consecutive NMP livers between 2018 and 2019 were included. All of the livers were perfused on the OrganOx metra device according to an institutional protocol. Transplant and perfusion data were collected prospectively.

Results.

Forty-five livers were transplanted after NMP. Five livers stem from donors after circulatory death and 31 (68.9%) from extended criteria donors. Mean (SD) cold ischemia time was 6.4 (2.3) h; mean (SD) total preservation time was 21.4 (7.1) h. Early allograft dysfunction (EAD) occurred in 13 of 45 (28.9%) patients. Perfusate aspartate aminotransferase (P = 0.008), alanine aminotransferase (P = 0.006), lactate dehydrogenase (P = 0.007) and their development over time, alkaline phosphatase (P = 0.013), and sodium (P = 0.016) correlated with EAD. Number of perfusate platelets correlated with cold ischemia time duration and were indicative for the occurrence of EAD. Moreover, von Willebrand Factor antigen was significantly higher in perfusates of EAD livers (P < 0.001), and Δ von Willebrand factor antigen correlated with EAD. Although perfusate lactate and glucose had no predictive value, EAD was more likely to occur in livers with lower perfusate pH (P = 0.008). ΔPerfusate alkaline phosphatase, Δperfusate aspartate aminotransferase, Δperfusate alanine aminotransferase, and Δperfusate lactate dehydrogenase correlated closely with model for early allograft function but not liver graft assessment following transplantation risk score. Bile parameters correlated with extended criteria donor and donor risk index.

Conclusions.

Biomarker assessment during NMP may help to predict EAD after liver transplantation. The increase of transaminases and lactate dehydrogenase over time as well as platelets and vWF antigen are important factors indicative for EAD.
Impact estimation on COVID-19 infections following school reopening in September 2020 in Italy
Authors: Fenga Livio , Galli Massimo
Published: June 2021

Background

Since its outbreak, CoViD-19 (formally known as 2019-nCoV) has been triggering many questions among public authorities, social organisms and school officials, as to when students should be allowed to return to school. Such a decision is critical and must take into account, other than its beneficial effects, also those associated with an increased exposition of the students to the virus, which, as a result, might spread at a faster rate. To date, in Italy, a few studies have rigorously investigated the correlation between school reopening and number of people tested positive to CoViD-19. Therefore, this paper aims to provide an assessment of such an impact as well as to illustrate the methodology followed.

Methods

Official daily data on the cumulative number of people tested positive to CoViD-19 – in conjunction with external information accounting for the different points in time schools reopened in the various Italian regions – have been employed to build a stochastic model of the type Seasonal Autoregressive Moving Average embodying external information.

Results

There was a statistically significant increase in the number of positive cases in all the Italian regions related to schools reopening. Such an increase occurred, in average, about 18.9 days after the schools have been reopened. Schools reopening have been significantly contributed to the diffusion of the pandemic, with an overall estimated impact of about 228,724 positive cases.

Conclusions

The results suggest the need for strict control of all in-school activities. This could be done by using, to a variable extent, all the non-pharmaceutical interventions available, such as limited access to school spaces, no overlapping practices between different sports in the same space, universal masking, bubble-size classroom. However, in many cases, such measures might not be a viable option, at least in the short run, nor be reasonably applicable. Therefore, whenever the established safety criteria could not be met, school buildings should remain closed.

Key Messages

Due to CoViD-19 pandemic, physical school attendance is at the center of an intense political and social debates;

schools reopening decision should be based on reliable and well maintained data-sets;

in the lack of quality data, it is advisable to use a portion of them, to reduce uncertainty.
Survival of vaccine-induced human milk SARS-CoV-2 IgG and IgA immunoglobulins across simulated human infant gastrointestinal digestion
Authors: Pieri Myrtani , Nicolaidou Vicky , Paphiti Irene , Pipis Spyros , Felekkis Kyriacos , Papaneophytou Christos
Published: June 2021

Four vaccines have been approved to date by the European Medicines Agency for the management of the COVID-19 pandemic in Europe, with all four being targeted to adults over 18 years of age. One way to protect the younger population such as infants or younger children until pediatric vaccines are licensed is through passive immunity via breastfeeding. Recent evidence points to the fact that human milk contains immunoglobulins (Ig) against the SARS-CoV-2 virus, both after natural infection or vaccination, but it is not known whether these antibodies can resist enzymatic degradation during digestion in the infant gastrointestinal (GI) tract or indeed protect the consumers. Here, we describe our preliminary experiments where we validated commercially available ELISA kits to detect IgA and IgG antibodies in human milk from two lactating mothers vaccinated with either the Pfizer/BioNTech or the Astra Zeneca vaccine, and the effect of a static in vitro digestion protocol on the IgA and IgG concentrations. Our data, even preliminary, provide an indication that the IgA antibodies produced after vaccination with the Pfizer/BioNTech vaccine resist the gastric phase but are degraded during the intestinal phase of infant digestion, whereas the IgGs are more prone to degradation in both phases of digestion. We are in the process of recruiting more individuals to further evaluate the vaccine induced immunoglobulin profile of breastmilk, and the extent to which these antibodies can resist digestion in the infant GI tract.
Two distinct networks containing position-tolerant representations of actions in the human brain
Authors: Yargholi Elahé , Hossein-Zadeh Gholam-Ali , Vaziri-Pashkam Maryam
Published: June 2021

Humans can recognize other people’s actions in the social environment. This action recognition ability is rarely hindered by the movement of people in the environment. The neural basis of this tolerance to changes in the position of observed actions is not fully understood. Here, we aimed to identify brain regions capable of generalizing representations of actions across different positions and investigate the representational content of these regions. fMRI data were recorded from twenty-two subjects while they were watching video clips of ten different human actions in Point Light Display format. Each stimulus was presented in either the upper or the lower visual fields. Multivoxel pattern analysis and a searchlight technique were employed to identify brain regions that contain position-tolerant action representation: linear support vector machine classifiers were trained with fMRI patterns in response to stimuli presented in one position and tested with stimuli presented in another position. Results of this generalization test showed above-chance classification in the left and right lateral occipitotemporal cortex, right intraparietal sulcus, and right post-central gyrus. To explore the representational content of these regions, we constructed models based on the objective measures of movements and human subjective judgments about actions. We then evaluated the brain similarity matrix from the cross-position classification analysis based on these models. Results showed cross-position classifications in the lateral occipito-temporal ROIs were more strongly related to the subjective judgments, while those in the dorsal parietal ROIs were more strongly related to the objective movements. An ROI representational similarity analysis further confirmed the separation of the dorsal and lateral regions. These results provide evidence for two networks that contain abstract representations of human actions with distinct representational content.
LongStitch: High-quality genome assembly correction and scaffolding using long reads
Authors: Coombe Lauren , Li Janet X , Lo Theodora , Wong Johnathan , Nikolic Vladimir , Warren René L , Birol Inanc
Published: June 2021

Background

Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

Results

LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM.

Conclusions

Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.
The membrane associated accessory protein is an adeno-associated viral egress factor
Authors: Elmore Zachary C. , Patrick Havlik L. , Oh Daniel K. , Vincent Heather A. , Asokan Aravind
Published: June 2021

Adeno-associated viruses (AAV) rely on helper viruses to transition from latency to lytic infection. Some recombinant AAV serotypes are secreted in a pre-lytic manner as extracellular vesicle (EV)-associated particles, although mechanisms underlying such are unknown. Here, we discover that the membrane-associated accessory protein (MAAP), expressed from a (+1) frameshifted open reading frame (ORF) in the AAV capsid (cap) gene, is a novel viral egress factor. MAAP contains a highly conserved, cationic amphipathic domain critical for AAV secretion. Wild type or recombinant AAV with a mutated MAAP start site (MAAPΔ) show markedly attenuated secretion and correspondingly, increased intracellular retention. Trans-complementation with recombinant MAAP restored extracellular secretion of multiple AAV/MAAPΔ serotypes. MAAP is sorted into recycling Rab11+ vesicles and strongly associates with EV markers upon fractionation. In addition to characterizing a novel viral egress factor, these studies highlight a prospective engineering platform to modulate secretion of AAV vectors or other EV-associated cargo.
A Robust High-throughput Fluorescent Polarization Assay for the Evaluation and Screening of SARS-CoV-2 Fusion Inhibitors
Authors: Yin Xinjian , Chen Litong , Yuan Siwen , Liu Lan , Gao Zhizeng
Published: June 2021

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a serious threat to global health. One attractive antiviral target is the membrane fusion mechanism employed by the virus to gain access to the host cell. Here we report a robust protein-based fluorescent polarization assay, that mimicking the formation of the six-helix bundle (6-HB) process during the membrane fusion, for the evaluation and screening of SARS-CoV-2 fusion Inhibitors. The IC50 of known inhibitors, HR2P, EK1, and Salvianolic acid C (Sal C) were measured to be 6 nM, 2.5 nM, and 8.9 µM respectively. In addition, we found Sal A has a slightly lower IC50 (3.9 µM) than Sal C. Interesting, simple caffeic acid can also disrupt the formation of 6-HB with sub-mM concentration. A pilot high throughput screening (HTS) a small marine natural product library validates the assay with a Z’ factor close to 0.8. We envision the current assay provides a convenient way to screen SARS-CoV-2 fusion inhibitor and assess their binding affinity.
Benchmarking UMI-based single cell RNA-sequencing preprocessing workflows
Authors: You Yue , Tian Luyi , Su Shian , Dong Xueyi , Jabbari Jafar S , Hickey Peter F , Ritchie Matthew E
Published: June 2021

Single-cell RNA sequencing (scRNA-seq) technologies and associated analysis methods have undergone rapid development in recent years. This includes methods for data preprocessing, which assign sequencing reads to genes to create count matrices for downstream analysis. Several packaged preprocessing workflows have been developed that aim to provide users with convenient tools for handling this process. How different preprocessing workflows compare to one another and influence downstream analysis has been less well studied.

Here, we systematically benchmark the performance of 9 end-to-end preprocessing workflows (Cell Ranger, Optimus, salmon alevin, kallisto bustools, dropSeqPipe, scPipe, zUMIs, celseq2 and scruff) using datasets with varying levels of biological complexity generated on the CEL-Seq2 and 10x Chromium platforms. We compare these workflows in terms of their quantification properties directly and their impact on normalization and clustering by evaluating the performance of different method combinations. We find that lowly expressed genes are discordant between workflows and observe that some workflows have systematic biases towards particular classes of genomics features. While the scRNA-seq preprocessing workflows compared varied in their detection and quantification of genes across datasets, after downstream analysis with performant normalization and clustering methods, almost all combinations produced clustering results that agreed well with the known cell type labels that provided the ground truth in our analysis.

In summary, the choice of preprocessing method was found to be less influential than other steps in the scRNA-seq analysis process. Our study comprehensively compares common scRNA-seq preprocessing workflows and summarizes their characteristics to guide workflow users.
Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense
Authors: Shirasawa Kenta , Kobayashi Nobuo , Nakatsuka Akira , Ohta Hideya , Isobe Sachiko
Published: June 2021

To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analyzed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars, respectively; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time (SMRT) sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read (stLFR) sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely-related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.
Impaired SorLA maturation and trafficking as a new mechanism for SORL1 missense variants in Alzheimer disease
Authors: Rovelet-Lecrux Anne , Feuillette Sebastien , Miguel Laetitia , Schramm Catherine , Pernet Ségolène , Ségalas-Milazzo Isabelle , Guilhaudis Laure , Rousseau Stéphane , Riou Gaëtan , Frébourg Thierry , Campion Dominique , Nicolas Gaël , Lecourtois Magalie
Published: June 2021

The SorLA protein, encoded by the SORL1 gene, is a major player in Alzheimer’s disease (AD) pathophysiology. Functional and genetic studies demonstrated that SorLA deficiency results in increased production of Aβ peptides, and thus a higher risk of AD. A large number of SORL1 missense variants have been identified in AD patients, but their functional consequences remain largely undefined. Here, we identified a new pathophysiological mechanism, by which rare SORL1 missense variants identified in AD patients result in altered maturation and trafficking of the SorLA protein. An initial screening, based on the overexpression of 71 SorLA variants in HEK293 cells, revealed that 15 of them (S114R, R332W, G543E, S564G, S577P, R654W, R729W, D806N, Y934C, D1535N, D1545E, P1654L, Y1816C, W1862C, P1914S) induced a maturation and trafficking-deficient phenotype. Three of these variations (R332W, S577P, and R654W) and two maturation-competent variations (S124R and N371T) were further studied in details in CRISPR/Cas9-modified hiPSCs. When expressed at endogenous levels, the R332W, S577P, and R654W SorLA variants also showed a maturation defective profile. We further demonstrated that these variants were largely retained in the endoplasmic reticulum, resulting in a reduction in the delivery of SorLA mature protein to the plasma membrane and to the endosomal system. Importantly, expression of the R332W and R654W variants in hiPSCs was associated with a clear increase of Aβ secretion, demonstrating a loss-of-function effect of these SorLA variants regarding this ultimate readout, and a direct link with AD pathophysiology. Furthermore, structural analysis of the impact of missense variations on SorLA protein indicated that impaired cellular trafficking of SorLA protein could be due to subtle variations of the protein 3D structure resulting from changes in the interatomic interactions.
Mental practice modulates functional connectivity between the cerebellum and the primary motor cortex
Authors: Monany Dylan Rannaud , Lebon Florent , Dupont William , Papaxanthis Charalambos
Published: June 2021

Our brain has the extraordinary capacity to improve motor skills through mental practice. Conceptually, this ability is attributed to internal forward models, which are neural networks that can predict the sensory consequences of motor commands. While the cerebellum is considered as a potential locus of internal forward models, evidence for its involvement in mental practice is missing. In our study, we employed single and dual transcranial magnetic stimulation technique to probe the level of corticospinal excitability and of cerebellar-brain inhibition, respectively, before and after a mental practice session or a control session. Motor skills (i.e., accuracy and speed) were measured using a sequential finger tapping-task. Here, we show that mental practice enhances both speed and accuracy. In parallel, the functional connectivity between the cerebellum and the primary motor cortex changes, with less inhibition from the first to the second, expressing the existence of neuroplastic changes within the cerebellum after mental practice. These findings reveal that the corticocerebellar loop is a major neural circuit for skill improvement after mental practice.
A computational screen for alternative genetic codes in over 250,000 genomes
Authors: Shulgina Yekaterina , Eddy Sean R.
Published: June 2021

The genetic code has been proposed to be a “frozen accident”, but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force which likely helped drive these codons to low frequency and enable their reassignment.