bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of sago pulp bokashi with addition of adhesive and drying methods
Authors: Maridhi D , Irfan  , Sulaiman Ismail
Published: February 2020

The purpose of this study was to assist the use of organic fertilizer at farmer level. This study used Group Randomised Design factorial with 3 factors. The first factor is the long drying time (T) consisting of 3 (three) levels, namely 0 day (T1), 1 day (T2), and 2 days (T3). The second factor is the drying type (P) consisting of two levels, namely indoor (P1) and outdoor (P2). The third factor is the adhesive material (A) consisting of three levels, namely 0% (A1), 2.5% (A2), and 5% (A3). Samples were then analysed for Most Probable Number (MPN), pH, carbon test, nitrogen test, C/N ratio, and crop test. The results showed drying time (T) has a very noticeable effect on Most Probable Number, moisture content, pH, carbon element, nitrogen element, C/N ratio, and crop test. The type of drying (P) has a very noticeable effect on Most Probable Number and crop test. The adhesive material (A) has a very noticeable effect on Most Probable Number, pH, nitrogen element, C/N ratio, and crop test. The prolonged interaction of drying and drying type (TP) is very noticeable in the Most Probable Number, and crop test. Prolonged interaction of drying and drying type (PA) is very real impact and crop test, as well as a noticeable effect on the temperature of the bokashi. Long-drying interactions and drying type (TPA) have a noticeable effect on the growing bokashi test temperature. The best bokashi granule was produced in T2P1A1 sample.
Changes in soil chemical properties in agroforestry system at USU Arboretum Kwala Bekala
Authors: Rizwan M , Rauf A , Rahmawaty  , Akub E N
Published: February 2020

One of the opportunities for utilization and optimization of the Arboretum land is by intensive cultivation of crops commodities to fulfil the needs of food, vegetables and other commodities. This study aims to analyse changes in soil nutrient status in four types of forest trees combined with agroforestry using soybean. Soil survey was carried out in area of USU Arboretum Kwala Bekala by soil sampling and then analyzed in the laboratory. Composite soil samples were taken from Jabon tree stands, (Anthocephalus cadamba Miq.), Gmelina (Gmelina arborea Roxb.), Rubber (Hevea brasiliensis.), and Mindi (Melia azedarach L.) at a depth of 0-30 cm. This sampling was carried out twice, namely before planting and after harvesting of soybeans. The results of soil analysis were assessed based on the criteria of Soil Research Center. Parameters observed for soil sample were N total (Kjeldahl method), phosphate (Bray method), C organic (Walkey and Black), Potassium and Sodium (Flame photometer), Calcium and Magnesium (AAS). The data obtained were analysed using a paired t test at the level of α 0.05. Almost all of the values of soil chemical properties gradually increased, and significant differences in those chemical properties were found between two condition, before and after the growing of soybean in four type stand of woods. Generally, Agroforestry system in four main stands (Rubber, Gmelina, Mindi and Jabon) with soybean for period 1-year can improve soil chemical fertility through increasing pH, C organic, N total, P available, Potassium, Na and Ca.
A study of changes in the quality of Lemea Block in various types of packaging materials during storage
Authors: Liyoni D , Dewi K H , Susanti L
Published: February 2020

Lemea is a typical Rejang tribe’s food made from chopped bamboo shoots and mixed with freshwater fish. Lemea block is a modification of the products so that it has a longer shelf life accompanied by proper packaging. The aim of this research is to obtain the effect of different types of packaging materials on the physical, chemical, microbiological and organoleptic properties of lemea blocks during storage. The research method used is Completely Randomized Design of one factor, namely the different types of packaging materials (paper packaging, plastic bottles from PET and Polypropylene) which are then analyzed using Analysis of Variance (ANOVA). Based on the results of this research, it was found that paper packaging type had significant effect on water content, pH, total plate number but no significant effect on color, aroma, texture and overall appearance. Types of PET and PP plastic bottles have no significant effect on water content, color, pH, total plate number, flavor, taste, texture and overall appearance of the lemea block during storage.
The effect of mychorrizal dose interactions with varieties on growth and yield of chili (Capsicum annum L.) in andisol soil Bener Meriah
Authors: Syafruddin  , Syamsuddin  , Syakur  , Jumini  , Halimursyadah  , Hasanuddin
Published: February 2020

This study aims to determine the interaction of mycorrhizal doses and varieties on the growth and yield of chili plants in Andisol soil. This research was conducted in Blang Kucak Village, Wih Pesam District, Bener Meriah Regency, Green House and Laboratory of Plant Physiology, Faculty of Agriculture, Syiah Kuala Darussalam University, Banda Aceh from January to May 2019. Analysis of the data used in this study was Randomized Block Design, with 3 x 2 factorial pattern with 3 replications. There are 2 series in this experiment namely Series A and Series B, series A is used for data collection of growth and yield of chili plants, while series B is used for data collection of mycorrhizal colonization. The factors observed in this study were mixed mycorrhizal bio-fertilizers and varieties. The dose of mycorrhizal bio-fertilizer used was control (without mycorrhizal), 5 g plant−1 and 10 g plant−1 and the varieties used were varieties of PM-999 and Perintis. The results showed a very significant interaction between mycorrhizal doses and varieties on the parameters of the number of productive branches, besides that there were significant interactions on plant height at 45 DAP, fruit weight, fruit length, number of fruits and yield potential (tons ha−1). The best combination was found in the treatment of doses of 10 g mycorrhizal plants−1 and Perintis varieties.
In-vitro propagation: application of gibberellic acid (GA3) in enhancing germination in ‘Jernang’ or ‘Dragon Blood’ (Daemonorops sp.)
Authors: Andini R , Luthfia N , Rahmawati M , Bakri S , Akhir J , Sulaiman M I
Published: February 2020

‘Dragon blood’ (Daemonorops sp.) is widely known as one of the indigenous Non-Forest Timber Products (NFTP) with high economical value in the deep forests of Indonesian and Malaysian Peninsula. The name referred to red resinous exudations from four distinct plant species that are endemic to various eco-geographical regions. It has been highly valued in Chinese traditional medicines or painting industries since the 14th century. Its resin is strongly related with active bio-compound with strong curing activities for stomach ulcers or intestines’ related cancer. However, jernang’s number of population in its natural habitats has been decreasing over the past three decades as a result of unsustainable harvesting. Thus, this has dramatically reduced its population and lower genetic diversity. Another challenge is that the period of seed germination is relatively long; namely up to 12 weeks as the seeds are usually covered with thick coat. Thus, immersion in water is prerequisite in order to support the germination. The best performance was shown with 1*24 h water imbibed seeds with GA3 (W = 2 mg l−1
). For in-vitro, various organs from 3-4 months old of young seedlings were employed as explants. However, current mixture of media did not promote an accelerated growth of explants. Therefore, applying another mixture of growth hormone is highly recommended in order to deliver better experimental result. This paper can be concluded as a basic pioneer in ex-situ conservation of ‘jernang’.
Improving fermented virgin coconut oil quality by using microwave heating
Authors: Khathir R , Agustina R , Hartuti S , Fahmi Z
Published: February 2020

The study aimed to improve the quality of fermented virgin coconut oil (FVCO) under microwave heating. The FVCO was collected from a local farmer in Aceh Besar District. A microwave oven at frequency of 2,450MHz and power of 800Wwas used to heat 40ml FVCO in a ceramic bowl by the variation heating time i.e. 40, 50, and 60s. The parameters observed were temperature, moisture content, free fatty acid (FFA), and peroxide value. Results showed that the quality of FVCO did not meet the quality standards such as Codex Alimentarius, Asian and Pacific Coconut Community (APCC), and the Indonesian National Standard (SNI). However, the study found that the microwave heating time had influenced the FVCO temperature significantly where the final temperature had reached 71-87°C. However, there were no significant influences of microwave heating time to the moisture, FFA, and peroxide value of FVCO. It could be caused by the short time used in this experiment; therefore, it is suggested to extend the heating time for further study.
Nutritional and sensory properties of shrimp analog made of fresh and saltwater fish surimi and tapioca
Authors: Arpi N , Fahrizal  , Rohaya S , Zahriati S
Published: February 2020

Fish spoilage can be prevented by processing, such as to process them into surimi. Surimi is utilized as a base material for manufacturing various kinds of processed products including shrimp analog. Shrimp analog can be used as an alternative food for those who are allergic to seafood, especially shrimp. This research studied the processing of surimi made into shrimp analog that has characteristics resembling natural shrimp. The purpose of this study was to determine the quality of shrimp analog made from surimi of some fish species and tapioca with different concentrations. This study used a randomized block design (RBD) factorial consisting of two factors. The first factor was surimi of various fish species (I) which were I1 = trigger fish, I2 = sardines, I3 = tilapia, and I4 = snakehead fish. The second factor was theconcentration of tapioca (T) comprised T1 = 6% and T2 = 8%. The shrimp analog samples then were analysed their water content, protein content, fat content, hedonic sensory test on color, aroma, texture and taste. The best treatment was obtained from shrimp analogmade of tilapia surimi with tapioca concentration of 8% (I3T2) which had water content of 51,97%, protein content of 15,17%, fat content of 0,45%, hedonic sensory value (scale 1-5) color of 3,69 (neutral-like), aroma of 2,77 (not like-neutral), texture of 3,31 (neutral), and taste of 3,37 (neutral)
Improvement of ruminal feed fermentation by addition of eucalyptus based mix essential oil
Authors: Kurniawati A , Wigati D N , Hasanah C , Yusiati L M
Published: February 2020

In vitro fermentation methodology was used in this research to explore the effect of mix essential oil (MEO) of eucalyptus (Melaleuca leucadendra (L.) and pine (Pinus merkusii (Jungh. and de Vriese), in ratio 3:1, on feed digestibility and parameter of ruminal feed fermentation. Mix essential oil was added and mix with feed particle to meet the end concentration of 100 μl/L of fermentation media. Incubation was done at 39°C for 24 h. Upon finished the incubation, gas produced were sampled for methane analysis. Residual feed was collected by filtration and then ben analysed the dry matter (DM) and organic matter (OM) content for calculation of DM and OM digestibility. Meanwhile filtrate also collected for determination of pH, ammonia, protozoa number and microbial protein synthesis. Data analysis showed MEO addition did not affect pH, ammonia concentration, DM and OM digestibility. Addition of MEO reduced methane production 24.62% (P<0.05), and increased microbial protein synthesis (P<0.05) from 133.89 mg/L to 189.66. Otherwise, protozoa number in MEO treatment was lower compared to control (P<0.05). In conclusion, mix essential oil of eucalyptus and pine essential oil up to level 100μl/L could be used as feed additive to improve the fermentation of feed in the rumen.
Is tubeless uniportal video-assisted thoracic surgery for pulmonary wedge resection a safe procedure?
Authors: Liu Chao-Yu , Hsu Po-Kuei , Leong Ka-I , Ting Chien-Kun , Tsou Mei-Yung
Published: February 2020

OBJECTIVES

Tubeless uniportal video-assisted thoracic surgery (VATS), using a uniportal approach and non-intubated anaesthesia while avoiding postoperative chest drain insertion, for patients undergoing thoracoscopic surgery has been demonstrated to be feasible in selected cases. However, to date, the safety of the procedure has not been studied.

METHODS

We reviewed consecutive patients undergoing non-intubated uniportal VATS for pulmonary wedge resection at 2 medical centres between August 2016 and October 2019. The decision to avoid chest drain insertion was made in selected candidates. For those candidates in whom a tubeless procedure was performed, postoperative chest X-rays (CXRs) were taken on the day of the surgery [operation (OP) day], on postoperative day 1 and 1–2 weeks later. The factors associated with abnormal CXR findings were studied.

RESULTS

Among 135 attempts to avoid chest drain insertion, 13 (9.6%) patients ultimately required a postoperative chest drain. Among 122 patients in which a tubeless procedure was performed, 26 (21.3%) and 47 (38.5%) had abnormal CXR findings on OP day and postoperative day 1, respectively. Among them, 3 (2.5%) patients developed clinically significant abnormal CXRs and required intercostal drainage. Primary spontaneous pneumothorax was independently associated with a higher risk of postoperative abnormal CXRs.

CONCLUSIONS

Tubeless uniportal VATS for pulmonary wedge resection can be safely performed in selected patients. Most patients with postoperative abnormal CXRs presented subclinical symptoms that spontaneously resolved; only 2.5% of patients with postoperative abnormal CXRs required drainage.
Change in prevalence of self-harm from 2002 to 2018 among Norwegian adolescents
Authors: Tørmoen Anita J , Myhre Martin , Walby Fredrik A , Grøholt Berit , Rossow Ingeborg
Published: February 2020

Background

Self-harm is prevalent among adolescents and associated with mental health problems and negative life-events. Few studies have examined changes in its prevalence related to these factors. This study explored whether changes in prevalence of self-harm among adolescents had occurred, and to what extent changes in associated factors may have contributed.

Methods

Two cross-sectional school-based surveys among adolescents (grades 8–10) in Norway were conducted in 2002 (N = 5842) and in 2017/18 (N = 29 063). Past year prevalence of self-harm and identical variables on risk factors was analyzed in hierarchical logistic regression to examine whether and to what extent changes in self-harm correlates could explain periodical change in prevalence of self-harm.

Results

An increase from 4.1% to 16.2% in self-harm prevalence was observed from 2002 to 2017/18. The increase was relatively larger among girls compared to boys and among 8th graders compared to 10th graders. Among the assessed risk factors for self-harm, depressive symptoms increased, while anti-social behavior, exposure to violent acts and drinking to intoxication decreased. The increase in depressive symptoms contributed to explain increase in self-harm. This contribution was outweighed by the decrease in other risk factors.

Conclusions

Self-harm prevalence increased 4-fold among Norwegian adolescents over a 15-year period. While exposure to several risk factors for self-harm changed substantially in this period, these risk factors could in sum not explain any of the increase in self-harm.
Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions
Authors: Fujitani Hirotsugu , Nomachi Manami , Takahashi Yu , Hasebe Yoshiaki , Eguchi Masahiro , Tsuneda Satoshi
Published: February 2020

In artificial engineered systems, nitrification is a key reaction that accounts for the removal of biological nitrogen. Recently, a single microbe capable of oxidizing ammonia to nitrate, known as a complete ammonia oxidizer (comammox), has been discovered. Although the abundance and diversity of comammox Nitrospira in engineered systems have been identified through molecular-based approaches, the enrichment and isolation of comammox Nitrospira remains a challenge. Therefore, the aim of this study was to enrich comammox Nitrospira from nitrifying granules, which were used to increase the efficiency of biological nitrogen removal in wastewater treatment plants. We sought to accomplish this through the use of a fixed-bed continuous feeding bioreactor. Fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing and qPCR of functional genes were utilized to monitor the growth of nitrifiers including comammox Nitrospira. Cloning of comammox amoA genes identified amoA phylogeny of enriched comammox Nitrospira. This work is an example demonstrating that continuous supply of low ammonium concentrations alongside biomass carriers is effective in cultivating comammox Nitrospira from engineered systems.
Hidden in plain sight: the overstated benefits and underestimated losses of potential implantations associated with advertised PGT-A success rates
Authors: Paulson Richard J
Published: February 2020

The utilization of preimplantation genetic testing for aneuploidy (PGT-A) has understandable intuitive appeal in reassuring the clinician that ‘everything possible’ has been done to assure the birth of a healthy baby. Whereas the development of the PGT-A technology is still in a relatively early stage, great strides have nevertheless been made in the understanding of the genetics of the preimplantation human embryo. The problem lies not in the progress that has been achieved, but rather, in the reality that PGT-A is being actively marketed as a mature technology. Those that market the technology overstate its benefits and underestimate the losses of potential implantations that are the consequence of the practice of PGT-A. The implication is that the PGT-A technology is accurate, has minimal errors and is ready to be applied to every case of IVF. This approach is not evidence-based. Substantial losses of potential implantations are even evident in the analysis of the numbers presented by marketing materials themselves. In order to provide accurate, evidence-based counseling for patients undergoing IVF, we need to apply an appropriate level of scientific scrutiny to the data that are available and apply PGT-A selectively to those cases in which the benefits clearly outweigh the costs.
T Lymphocyte Subsets Associated With Prevalent Diabetes in Veterans With and Without Human Immunodeficiency Virus
Authors: Bailin Samuel S , McGinnis Kathleen A , McDonnell Wyatt J , So-Armah Kaku , Wellons Melissa , Tracy Russell P , Doyle Margaret F , Mallal Simon , Justice Amy C , Freiberg Matthew S , Landay Alan L , Wanjalla Celestine , Koethe John R
Published: February 2020

Background

A higher proportion of circulating memory CD4+ T cells is associated with prevalent diabetes mellitus in the general population. Given the broad changes in adaptive immunity, including memory T-cell expansion, and rising prevalence of diabetes in the human immunodeficiency virus (HIV) population, we assessed whether similar relationships were present in persons with HIV (PWH).

Methods

Multiple CD4+ and CD8+ T-cell subsets were measured by flow cytometry, and prevalent diabetes cases were adjudicated by 2 physicians for PWH and HIV-negative participants in the Veterans Aging Cohort Study. Multivariable logistic regression models evaluated the association of T-cell subsets and diabetes stratified by HIV status, adjusted for cytomegalovirus serostatus and traditional risk factors.

Results

Among 2385 participants (65% PWH, 95% male, 68% African American), higher CD45RO+ memory CD4+ T cells and lower CD38+ CD4+ T cells were associated with prevalent diabetes, and had a similar effect size, in both the PWH and HIV-negative (P ≤ .05 for all). Lower CD38+CD8+ T cells were also associated with diabetes in both groups.

Conclusions

The CD4+ and CD8+ T-cell subsets associated with diabetes are similar in PWH and HIV-negative individuals, suggesting that diabetes in PWH may be related to chronic immune activation.
Equine-Assisted Therapy for Veterans with PTSD: Manual Development and Preliminary Findings
Authors: Arnon Shay , Fisher Prudence W , Pickover Alison , Lowell Ari , Turner J Blake , Hilburn Anne , Jacob-McVey Jody , Malajian Bonnie E , Farber Debra G , Hamilton Jane F , Hamilton Allan , Markowitz John C , Neria Yuval
Published: February 2020

Introduction

Equine-assisted therapy (EAT) for post-traumatic stress disorder (PTSD) has attracted great interest despite lacking empirical support, a manual, and a standardized protocol. Our team of experts in EAT and PTSD developed an eight-session group EAT treatment protocol for PTSD (EAT-PTSD) and administered it to two pilot groups of military veterans to assess initial effects.

Materials and Methods

We describe the development of the treatment manual, which was used with two pilot groups of veterans. Protocol safety, feasibility, and acceptability were assessed by reported adverse events, treatment completion rates, and self-rated patient satisfaction. Preliminary data on PTSD, depressive, and anxiety symptoms and quality of life were collected pretreatment, midpoint, post-treatment, and at 3-month follow up.

Results

No adverse events were recorded. All patients completed treatment, reporting high satisfaction. Preliminary data showed decreases in clinician-assessed PTSD and depressive symptoms from pre to post-treatment and follow-up (medium to large effect sizes, d = .54–1.8), with similar trends across self-report measures (d = 0.72–1.6). In our pilot sample, treatment response and remission varied; all patients showed some benefit post-treatment, but gains did not persist at follow-up.

Conclusions

This article presents the first standardized EAT protocol. Highly preliminary results suggest our new manualized group EAT-PTSD appears safe, well-regarded, and well-attended, yielding short-term benefits in symptomatology and quality of life if unclear length of effect. Future research should test this alternative treatment for PTSD more rigorously.
Duplications and Functional Convergence of Intestinal Carbohydrate-Digesting Enzymes
Authors: Brun Antonio , Mendez-Aranda Daniel , Magallanes Melisa E , Karasov William H , Martínez del Rio Carlos , Baldwin Maude W , Caviedes-Vidal Enrique
Published: February 2020

Vertebrate diets and digestive physiologies vary tremendously. Although the contribution of ecological and behavioral features to such diversity is well documented, the roles and identities of individual intestinal enzymes shaping digestive traits remain largely unexplored. Here, we show that the sucrase-isomaltase (SI)/maltase-glucoamylase (MGAM) dual enzyme system long assumed to be the conserved disaccharide and starch digestion framework in all vertebrates is absent in many lineages. Our analyses indicate that independent duplications of an ancestral SI gave rise to the mammalian-specific MGAM, as well as to other duplicates in fish and birds. Strikingly, the duplicated avian enzyme exhibits similar activities to MGAM, revealing an unexpected case of functional convergence. Our results highlight digestive enzyme variation as a key uncharacterized component of dietary diversity in vertebrates.
Ex vivo ultrasonic samples of human brain tumors in the molecular era
Authors: Kirby Alastair J , Lavrador José P , Bodi Istvan , Vergani Francesco , Bhangoo Ranjeev , Ashkan Keyoumars , Finnerty Gerald T
Published: February 2020

Background

Gliomas are composed of multiple clones of tumor cells. This intratumor heterogeneity contributes to the ability of gliomas to resist treatment. It is vital that gliomas are fully characterized at a molecular level when a diagnosis is made to maximize treatment effectiveness.

Methods

We collected ultrasonic tissue fragments during glioma surgery. Large tissue fragments were separated in the operating theater and bathed continuously in oxygenated artificial cerebrospinal fluid to keep them alive. The ex vivo tissue fragments were transferred to a laboratory and incubated in 5-aminolevulinic acid (5-ALA). 5-ALA is metabolized to Protoporphyrin IX (PpIX), which accumulates in glioma cells and makes them fluorescent. The molecular and neuropathological features of the PpIX fluorescent ultrasonic tissue fragments were studied.

Results

We show that PpIX fluorescence can rapidly identify tissue fragments infiltrated by glioma in the laboratory. Ultrasonic tissue fragments from the tumor core provided molecular and neuropathological information about the glioma that was comparable to the surgical biopsy. We characterized the heterogeneity within individual gliomas by studying ultrasonic tissue fragments from different parts of the tumor. We found that gliomas exhibit a power relationship between cellular proliferation and tumor infiltration. Tissue fragments that deviate from this relationship may contain foci of more malignant glioma. The methylation status of the O6-methylguanine DNA methyltransferase gene promoter varied within each glioma.

Conclusions

Ex vivo ultrasonic tissue fragments can be rapidly screened for glioma infiltration. They offer a viable platform to characterize heterogeneity within individual gliomas, thereby enhancing their diagnosis and treatment.
Petrogenesis of the Ulungur Intrusive Complex, NW China, and Implications for Crustal Generation and Reworking in Accretionary Orogens
Authors: Tang Gong-Jian , Wang Qiang , Wyman Derek A , Dan Wei , Ma Lin , Zhang Hai-Xiang , Zhao Zhen-Hua
Published: February 2020

Accretionary orogens are characterized by voluminous juvenile components (recently derived from the mantle) and knowing the origin(s) of such components is vital for understanding crustal generation. Here we present field and petrological observations, along with mineral chemistry, zircon U–Pb age and Hf–O isotope data, and whole rock geochemical and Sr–Nd isotopic data for the c.320 Ma Ulungur intrusive complex from the Central Asian Orogenic Belt. The complex consists of two different magmatic series: one is characterized by medium- to high-K calc-alkaline gabbro to monzogranite; the other is defined by peralkaline aegirine–arfvedsonite granitoids. The calc-alkaline and peralkaline series granitoids have similar depleted mantle-like Sr–Nd–Hf isotopic compositions, but they have different zircon δ18O values: the calc-alkaline series have mantle-like δ18O values with mean compositions ranging from 5·2 ± 0·5‰ to 6·0 ± 0·9‰ (2SD), and the peralkaline granitoids have low δ18O values ranging from 3·3 ± 0·5‰ to 3·9 ± 0·4‰ (2SD). The calc-alkaline series were derived from a hydrous sub-arc mantle wedge, based on the isotope and geochemical compositions, under garnet peridotite facies conditions. This study suggests that the magmas underwent substantial differentiation, ranging from high pressure crystallization of ultramafic cumulates in the lower crust to lower pressure crystallization dominated by amphibole, plagioclase and minor biotite in the upper crust. The peralkaline series rocks are characterized by δ18O values lower than the mantle and enrichment of high field strength elements (HFSEs) and heavy rare earth elements (HREEs). They likely originated from melting of preexisting hydrothermally altered residual oceanic crust in the lower crust of the Junggar intra-oceanic arc. Early crystallization of clinopyroxene and amphibole was inhibited owing to their low melting temperature, leading to HFSEs and HREEs enrichment in residual peralkaline melts during crystallization of a feldspar-dominated mineral assemblage. Thus, the calc-alkaline and peralkaline series represent episodes of crust generation and reworking, respectively, demonstrating that the juvenile isotopic signature in accretionary orogens can be derived from diverse source rocks. Our results show that reworking of residual oceanic crust also plays an important role in continental crust formation for accretionary orogens, which has not previously been widely recognized.
Quantification of the pace of biological aging in humans through a blood test: The DunedinPoAm DNA methylation algorithm
Authors: Belsky DW , Caspi A , Arseneault L , Baccarelli A , Corcoran D , Gao X , Hannon E , Harrington HL , Rasmussen LJH , Houts R , Huffman K , Kraus WE , Kwon D , Mill J , Pieper CF , Prinz J , Poulton R , Schwartz J , Sugden K , Vokonas P , Williams BS , Moffitt TE
Published: February 2020

Biological aging is the gradual, progressive decline in system integrity that occurs with advancing chronological age, causing morbidity and disability. Measurements of the pace of aging are needed to serve as surrogate endpoints in trials of therapies designed to prevent disease by slowing biological aging. We report a blood DNA-methylation measure that is sensitive to variation in the pace of biological aging among individuals born the same year. We first modeled longitudinal change in 18 biomarkers tracking organ-system integrity across 12 years of follow-up in the Dunedin birth cohort. Rates of change in each biomarker were composited to form a measure of aging-related decline, termed Pace of Aging. Elastic-net regression was used to develop a DNA-methylation predictor of Pace of Aging, called DunedinPoAm for Dunedin (P)ace (o)f (A)ging (m)ethylation. Validation analyses showed DunedinPoAm was associated with functional decline in the Dunedin Study and more advanced biological age in the Understanding Society Study, predicted chronic disease and mortality in the Normative Aging Study, was accelerated by early-life adversity in the E-risk Study, and DunedinPoAm prediction was disrupted by caloric restriction in the CALERIE trial. DunedinPoAm generally outperformed epigenetic clocks. Findings provide proof-of-principle for DunedinPoAm as a single-time-point measure of a person’s pace of biological aging.
Concurrent MEG-articulography for investigating neuromotor control of speech articulation
Authors: Johnson Blake , Meng Qinqing , Anastasopoulou Ioanna , Ratko Louise , Szalay Tunde , Proctor Michael , Jobst Cecilia , van Lieshout Pascal , Cheyne Douglas
Published: February 2020

Articulography and functional neuroimaging are two major tools for studying the neurobiology of speech production. Until now, however, it has generally not been possible to use both in the same experimental setup because of technical incompatibilities between the two methodologies. Here we describe results from a novel articulography system dubbed Magneto-articulography for the Assessment of Speech Kinematics (MASK), used for the first time to obtain kinematic profiles of oro-facial movements during speech together with concurrent magnetoencephalographic (MEG) measurements of neuromotor brain activity. MASK was used to characterise speech kinematics in a healthy adult, and the results were compared to measurements from the same participant with a conventional electromagnetic articulography (EMA) setup. We also characterised speech movement kinematics with MASK in a group of ten typically developing children, aged 8-12 years. Analyses targeted the gestural landmarks of the utterances /ida/, /ila/ and reiterated productions of /pataka/. These results demonstrate that the MASK technique can be used to reliably characterise movement profiles and kinematic parameters that reflect development of speech motor control, together with MEG measurements of brain responses from speech sensorimotor cortex. This new capability sets the stage for cross-disciplinary efforts to understand the developmental neurobiology of human speech production.
Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates
Authors: Cottrell Christopher A. , van Schooten Jelle , Bowman Charles A. , Yuan Meng , Oyen David , Shin Mia , Morpurgo Robert , van der Woude Patricia , van Breemen Marielle , Torres Jonathan L. , Patel Raj , Gross Justin , Sewall Leigh M. , Copps Jeffrey , Ozorowski Gabriel , Nogal Bartek , Sok Devin , Rakasz Eva G. , Labranche Celia , Vigdorovich Vladimir , Christley Scott , Carnathan Diane G. , Sather D. Noah , Montefiori David , Silvestri Guido , Burton Dennis R. , Moore John P. , Wilson Ian A. , Sanders Rogier W. , Ward Andrew B. , van Gils Marit J.
Published: February 2020

The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.
Effects of a postnatalAtrxconditional knockout in neurons on autism-like behaviours in male and female mice
Authors: Martin-Kenny Nicole , Bérubé Nathalie G.
Published: February 2020

Background

Alpha-thalassemia/mental retardation, X-linked, orATRX, is an autism susceptibility gene that encodes a chromatin remodeler. Mutations ofATRXresult in the ATR-X intellectual disability syndrome and have been identified in autism spectrum disorder (ASD) patients. The mechanisms by whichATRXmutations lead to autism and autistic-like behaviours are not yet known. To address this question, we generated mice with postnatalAtrxinactivation in excitatory neurons of the forebrain and performed a battery of behavioural assays that assess autistic-like behaviours.

Methods

Male and female mice with a postnatal conditional knockout ofAtrxwere tested in a battery of behavioural tests that assess autistic features. We utilized paradigms that measure social behaviour, repetitive and stereotyped behaviours, as well as sensory gating. Statistics were calculated by two-way repeated measures ANOVA with Sidak’s multiple comparison test or unpaired Student’s T-tests as indicated.

Results

The behaviour tests revealed no significant differences betweenAtrx-cKO and control mice. We identified sexually dimorphic changes in odor habituation and discrimination; however, these changes did not correlate with social deficits. We additionally observed sex-specific differences in sociability, vertical episodes, and acoustic startle response when results were analyzed by sex.

Conclusion

The postnatal knockout ofAtrxin forebrain excitatory neurons does not lead to autism-related behaviours in male or female mice.
A Multicenter Preclinical MRI Study: Definition of Rat Brain Relaxometry Reference Maps
Authors: Deruelle Tristan , Kober Frank , Perles-Barbacaru Adriana , Delzescaux Thierry , Noblet Vincent , Barbier Emmanuel L. , Dojat Michel
Published: February 2020

Similarly to human population imaging, there are several well-founded motivations for animal population imaging, the most notable being the improvement of the validity of statistical results by pooling a sufficient number of animal data provided by different imaging centers. In this paper, we demonstrate the feasibility of such a multicenter animal study, sharing raw data from forty rats and processing pipelines between four imaging centers. As specific use case, we considered the estimation of T1 and T2 maps for the healthy rat brain at 7T. We quantitatively report about the variability observed across two data provider centers and evaluate the influence of image processing steps on the final maps, by using three fitting algorithms from three centers. Finally, to derive relaxation time values per brain area, two multi-atlas segmentation pipelines from different centers were executed on two different platforms. In this study, the impact of the acquisition was 2.21% (not significant) and 9.52% on T1 and T2 estimates while the impact of the data processing pipeline was not significant (1.04% and 3.33%, respectively). In addition, the computed normality values can serve as relaxometry reference maps to explore differences to animal models of pathologies.
PICH function is required for organization of SUMOylated proteins on mitotic chromosomes
Authors: Hassebroek Victoria A. , Park Hyewon , Pandey Nootan , Lerbakken Brooklyn T. , Aksenova Vasilisa , Arnaoutov Alexei , Dasso Mary , Azuma Yoshiaki
Published: February 2020

Proper chromosome segregation is essential for faithful cell division and if not maintained results in defective cell function caused by abnormal distribution of genetic information. Polo-like kinase 1 interacting checkpoint helicase (PICH) is a DNA translocase essential in chromosome bridge resolution during mitosis. Its function in resolving chromosome bridges requires both DNA translocase activity and ability to bind chromosomal proteins modified by Small Ubiquitin-like modifier (SUMO). However, it is unclear how these activities are cooperating to resolve chromosome bridges. Here, we show that PICH specifically promotes the organization of SUMOylated proteins like SUMOylated TopoisomeraseIIα (TopoIIα) on mitotic chromosomes. Conditional depletion of PICH using the Auxin Inducible Degron (AID) system resulted in the retention of SUMOylated chromosomal proteins, including TopoIIα, indicating that PICH functions to control proper association of these proteins with chromosomes. Replacement of PICH with its mutants showed that PICH is required for the proper organization of SUMOylated proteins on chromosomes.In vitroassays showed that PICH specifically attenuates SUMOylated TopoIIα activity using its SUMO-binding ability. Taken together, we propose a novel function of PICH in remodeling SUMOylated proteins to ensure faithful chromosome segregation.

Summary Statement

Polo-like kinase interacting checkpoint helicase (PICH) interacts with SUMOylated proteins to mediate proper chromosome segregation during mitosis. The results demonstrate that PICH controls association of SUMOylated chromosomal proteins, including Topoisomerase IIα, and that function requires PICH translocase activity and SUMO binding ability.
Duplications drive diversity inBordetella pertussison an underestimated scale
Authors: Abrahams Jonathan S. , Weigand Michael R. , Ring Natalie , MacArthur Iain , Peng Scott , Williams Margaret M. , Bready Barrett , Catalano Anthony P. , Davis Jennifer R. , Kaiser Michael D. , Oliver John S. , Sage Jay M. , Bagby Stefan , Tondella M. Lucia , Gorringe Andrew R. , Preston Andrew
Published: February 2020

Bacterial genetic diversity is often described using solely base pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplications of genomic loci are thought to be widespread among bacteria but due to their often intractable size and instability, comprehensive studies of the range and genome dynamics of these mutations are rare. We define a methodology to investigate duplications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach withBordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for duplications to occur. Analysis of genome sequence data for 2430B. pertussisisolates identified 272 putative duplications, of which 94% were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of duplications, suggesting unstable and sporadic characteristics. Genome instability was further described in-vitro using long read sequencing via the Nanopore platform. Clonally derived laboratory cultures produced heterogenous populations containing multiple structural variants. Short read data was used to predict 272 duplications, whilst long reads generated on the Nanopore platform enabled the in-depth study of the genome dynamics of tandem duplications inB. pertussis. Our work reveals the unrecognised and dynamic genetic diversity ofB. pertussisand, as the complexity of theB. pertussisgenome is not unique, highlights the need for a holistic and fundamental understanding of bacterial genetics.
Method forin vivoassessment of cancer tissue inhomogeneity and accurate histology-like morphological segmentation based on Optical Coherence Elastography
Authors: Plekhanov Anton A. , Sirotkina Marina A. , Sovetsky Alexander A. , Gubarkova Ekaterina V. , Kuznetsov Sergey S. , Matveyev Alexander L. , Matveev Lev A. , Zagaynova Elena V. , Gladkova Natalia D. , Zaitsev Vladimir Y.
Published: February 2020

We present a non-invasive method based on Optical Coherence Elastography (OCE) enabling thein vivosegmentation of morphological tissue constituents, in particular, monitoring of morphological alterations during both tumor development and its response to therapies. The method uses compressional OCE to reconstruct tissue stiffness map as the first step. Then the OCE-image is divided into regions, for which the Young’s modulus (stiffness) falls in specific ranges corresponding to the morphological constituents to be discriminated. These stiffness ranges (characteristic “stiffness spectra”) are initially determined by careful comparison of the “gold-standard” histological data and the OCE-based stiffness map for the corresponding tissue regions. After such precalibration, the results of morphological segmentation of OCE-images demonstrate a striking correlation with the histological results in terms of percentage of the segmented zones. To demonstrate high sensitivity of the OCE-method and its excellent correlation with conventional histological segmentation we present results obtainedin vivoon a murine model of breast cancer in comparative experimental study of the efficacy of two anti-tumor chemotherapeutic drugs with different mechanisms of action. The new technique allowedin vivomonitoring and quantitative segmentation of (i) viable, (ii) dystrophic, (iii) necrotic tumor cells and (iv) edema zones very similar to morphological segmentation of histological images. Numerous applications in other experimental/clinical areas requiring rapid, nearly real-time, quantitative assessment of tissue structure can be foreseen.
Rational arbitration between statistics and rules in human sequence processing
Authors: Maheu Maxime , Meyniel Florent , Dehaene Stanislas
Published: February 2020

Detecting and learning temporal regularities is essential to accurately predict the future. A long-standing debate in cognitive science concerns the existence of a dissociation, in humans, between two systems, one for handling statistical regularities governing the probabilities of individual items and their transitions, and another for handling deterministic rules. Here, to address this issue, we used finger tracking to continuously monitor the online build-up of evidence, confidence, false alarms and changes-of-mind during sequence processing. All these aspects of behaviour conformed tightly to a hierarchical Bayesian inference model with distinct hypothesis spaces for statistics and rules, yet linked by a single probabilistic currency. Alternative models based either on a single statistical mechanism or on two non-commensurable systems were rejected. Our results indicate that a hierarchical Bayesian inference mechanism, capable of operating over distinct hypothesis spaces for statistics and rules, underlies the human capability for sequence processing.
Probing the effect of glycosaminoglycan depletion on integrin interactions with collagen I fibrils in the native ECM environment
Authors: Roth Jonathan , Hoop Cody L. , Williams Jonathan K. , Hayes Robert , Baum Jean
Published: February 2020

Fibrillar collagen–integrin interactions in the extracellular matrix (ECM) regulate a multitude of cellular processes and cell signalling. Collagen I fibrils serve as the molecular scaffolding for connective tissues throughout the human body and are the most abundant protein building blocks in the ECM. The ECM environment is diverse, made up of several ECM proteins, enzymes, and proteoglycans. The contents of the ECM environment are modulated by disease and aging and may influence these critical collagen–integrin interactions. In particular, glycosaminoglycans (GAGs), anionic polysaccharides that decorate proteoglycans, become depleted in the ECM with natural aging and their mis-regulation has been linked to cancers and other diseases. The impact of GAG concentration in the ECM environment on collagen interactions is not well understood. Here, we integrate protein adhesion assays with liquid high resolution atomic force microscopy (AFM) to assess the affects of GAG depletion on the interaction of collagen I fibrils with the integrin α2I domain. Adhesion assays demonstrate that α2I preferentially binds to GAG-depleted collagen I fibrils. By amplitude modulated AFM in air and in solution, we find that GAG-depleted collagen I fibrils retain structural features of the native fibrils, including their characteristic D-banding pattern, a key structural motif. AFM fast force mapping in solution shows that GAG depletion reduces the stiffness of individual fibrils, lowering the indentation modulus by half compared to native fibrils. Together these results shed new light on how GAGs influence collagen I fibril– integrin interactions and may aid in strategies to treat diseases that result from GAG misregulation.

Statement for broader audience

Aging and disease result in mis-regulation of glycosaminoglycan (GAG) levels in the extracellular matrix (ECM), which may affect fibrillar collagen interactions that are vital for cellular processes. Here, we characterize the impact of GAG depletion on collagen–integrin α2I domain interactions and collagen fibril topography and stiffness. We show that GAG depletion increases collagen–α2I binding and reduces stiffness in comparison to native fibrils. These results may inform on strategies for treating GAG mis-regulation.
Widespread Recombination Suppression Facilitates Plant Sex Chromosome Evolution
Authors: Rifkin Joanna L. , Beaudry Felix E.G. , Humphries Zoë , Choudhury Baharul I. , Barrett Spencer C.H. , Wright Stephen I.
Published: February 2020

1

Classical models suggest recombination rates on sex chromosomes evolve in a stepwise manner to localize the inheritance of sexually antagonistic variation in the sex where it is beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plantRumex hastatulus, a species with a young neo-sex chromosome found in part of its geographical range. We found that the ancestral sex-linked region is located in a large region characterized by low recombination. Furthermore, comparison between the recombination landscape of the neo-sex chromosome and its autosomal homologue indicates that low recombination rates preceded sex linkage. Our findings suggest that ancestrally low rates of recombination have facilitated the formation and evolution of heteromorphic sex chromosomes.