bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of good manufacturing practices (GMPs) in traditional fish cracker home industries in Pangkahkulon-Gresik, East Java, Indonesia
Authors: Fuad M A Z , Iranawati F , Kartikaningsih H
Published: November 2021

Fish crackers are one of the very popular snacks in Indonesia. The production processed of this snack, which starts from handling of raw materials to packaging, must be in accordance with food safety that has been determined by the government through the Food and Drug Supervisory Agency. This study aims to evaluate the implementation of Good Manufacturing Practices (GMPs) in 5 fish cracker home industries in Pangkahkulon Village, Ujungpangkah, Gresik District. The evaluation method used is based on the Indonesia Minister of Industry Regulation No.75/M-Ind/Per/7/2010 and regulation of the head of BPOM No. HK03.1.23.04.12.2200 of 2012, both was concerning the procedures for Inspection of Home Industry Food Production Facilities. The results indicate that the home industry has not implemented GMPs in accordance with BPOM regulations so that the five SMEs can be categorized at the lowest level (level IV). Some critical findings include the absence of closed waste bins, animals and pets that roam around the production site, do not have a record of the production process and do not have a label that shows the list of ingredients used along with the nutritional value available.
Mortality and exploitation rate of some reef fish in Ternate Island Waters
Authors: Rumagia F , Kaidati B , Darmawaty  , Nisaa K
Published: November 2021

Fish population dynamics are determined by the balance between population increase resulted from growth and addition of new individuals (recruitment), and population decrease due to fishing mortality and natural mortality. It is important to understand fish resources condition, including their change pattern caused by pressures on coral reef fisheries resource in coastal area of Ternate Island. This research aimed to analyze mortality and exploitation rate of several reef fishes that caught at coastal area of Ternate Island. Stock assessment method was used to determine the mortality and exploitation rate of some reef fishes. Study results showed that the fishing mortality of the sample species was lower than their natural mortality, while the exploitation rate results also showed the same condition those found in mortality rate, where the fish with high growth coefficient tended to have high mortality rates.
Sepat Siam fish community (Trichopodus pectoralis Regan, 1910) in Semayang Lake, East Kalimantan
Authors: Samuel  , Dwirastina M , Ditya Y C
Published: November 2021

Siam sepat (Trichopodus pectoralis) is a fish that lives with the characteristics of its life in mainland public waters such as rivers, lakes and flooded swamps. The Siam sepat is classified as a consumption fish, has morphological characteristics with a small mouth with a pointed snout and a flat body shape. The research was conducted from March to October 2018 in Semayang Lake, East Kalimantan. Fish samples obtained from fishermen’s catch using fishing gear, including nets, nets, tangkul, scoops and traps. This study used an enumerator to record the length and weight of the fish. The results of the research analysis showed that the size of the individuals who dominate the Siam sepat fish population is at the size of 14.0-17.0 cm (60.8%), the allometric growth pattern (-) with the equation W = 0.0393 * L2.6409. The size of the first caught (Lc) of the Siam Sepat fish was 17.31 cm, the maximum average length (L∞) was 22.75 cm and the growth coefficient (K) was 0.78 per year. Natural mortality (M) and fishing mortality (F) were 1.64 and 2.64 per year, respectively. Thus the rate of exploitation (E) = 0.62 has exceeded the optimum value indicating that the fishing effort of Siamese septic fish in Lake Semayang has occurred overfishing.
Environmental conditions of the landscape functioning in the Pribaikalskii National Park: historical perspective
Authors: Atutova Zh V , Li Zehong
Published: November 2021

The history of the economic development of the valley complexes of the Goloustnaya River basin is considered. Forestry and agricultural activities are designated as the main activities developed by the local population. Fluctuation changes in the intensity of their implementation are highlighted, specifically. the slowly developing process of economic development of valley landscapes due to low population in the second half o f the 17th century and until the first half of the 20th century; expansion of agricultural land and growth of industrial development of forest resources, starting from the middle of the 20th century until the end of the 1980s; and a decrease in economic activities since the end of the last century, which is connected both with the state reorganization of the country’s economy and with creation of specially protected natural territories within the studied area. The valley complexes of the Goloustnaya River are at risk from the recreational development of coastal areas of Lake Baikal that have been actively developing in recent years. Taiga landscapes of the upper and middle reaches of the river are at risk of spreading forest fires. Negative consequences from economic activities have been contributing to a significant anthropogenic transformation of landscapes of the Pribaikalskii National Park for a long period.
Assessment of soil contamination using remote sensing data in the Tamsag-Bulag oil field, Mongolia
Authors: Gantumur S , Kharitonova G V , Stepanov A S , Dubrovin K N
Published: November 2021

Although field surveus represent an essential method for determining oil contamination of soils and soil cover, the use of remote sensing techniques has become one of the main trends over recent years due to their economic and temporary advantages. The fundamental basis of this approach is the assessment of changes in vegetation cover by vegetation indices as indicator. In this study, the problems of assessment of the soil cover contamination during oil production are considered. It is aimed to select and evaluate objective criteria for soil cover contamination with oil in the Tamsag–Bulag field (Eastern Gobi, Mongolia). For this purpose, during the period of maximum vegetation growth, various vegetation indices were investigated at test sites (4 km2) from 2015 to 2019. The Normalized Difference Vegetation Index (NDVI) and Soil Adjusted Vegetation Index (SAVI) were used with Sentinel-2 and MODIS of the Terra satellite images at 30 and 250 m resolution, respectively. The monitoring of the land quality with satellite images via NDVI and SAVI allows us to assess the area of oil contamination of the soils and soil cover. The significant increase in the values of the NDVI and SAVI at a distance of more than 4 km from the center of the Tamsag-Bulag oil field is shown. The obtained results indicate the possibility of assessment and monitoring the state of the oil-ed territories of the Eastern Gobi by NDVI и SAVI using satellite images.
Species composition of mosses of wetland ecosystems of the Bolonsky Reserve
Authors: Kuptsova V A
Published: November 2021

This paper presents the data on the moss species diversity in wetlands of the Bolonsky State Nature Reserve. The spectrum includes 45 species from 18 genera, 15 families and 5 orders belonging to Polytrichopsida, Bryopsida and Sphagnopsida classes. The Polytrichopsida class includes 3 species, Bryopsida - 19 species and Sphagnopsida - 23 species. The most numerous in species composition was the Sphagnaceae family.
The larch forest of the “Bastak” State Nature Reserve (Jewish autonomous region)
Authors: Lonkina E S , Rubtsova T A , Gorelov V A
Published: November 2021

The article presents the information about the current state of the larch forests of the “Bastak”. State Nature Reserve The area, ecological and cenotic conditions of growth are determined, the classification of the studied plant communities is presented, a brief description of the forest structure is given. The current state of the larch forests of the “Bastak” State Nature Reserve can be assessed as fairly stable. Currently, larch forests occupy within 25 % of the forested area. The most widespread area is occupied by lowland larch forests (94 %). Mountain larch forests are derived plant communities formed after forest cutting in fir-spruce forests.
The ecological tourism in the islands of Peter the Great Bay (Sea of Japan)
Authors: Mayorova L A , Varchenko L I
Published: November 2021

The article considers the objects and main types of ecological tourism on the islands of Peter the Great Bay (Sea of Japan). The accelerated pace of socio-economic development in the Primorsky Krai, its strengthening cooperation with the countries of the Asia-Pacific region (ATR), the annual holding of economic summits in Vladivostok make the tourism industry a promising path of the economic development. The Primorsky Krai is a leader in the development of tourism and recreation in the Far East. Ecological tourism is a journey through nature. The main types of ecological tourism are scientific, educational and recreational ones. A trip to nature should be combined with respect for the latter, the study, protection, and restoration of unique landscapes. Ecological tours are offered to vacationers as an alternative to traditional long-distance travels to foreign countries. The Peter the Great Bay is the largest bay in the Sea of Japan at the coast of Russia. The large and small islands of the bay, the island territories of Vladivostok (Russkiy, Popova and Reineke) and the adjacent waters of the Sea of Japan are natural complexes with a unique nature and favorable climate. Sandy beaches and amazingly beautiful shores, convenient bays and inlets, are good objects for the development of various types of ecological tourism.
Vitality structure of Acer negundo populations in an urban environment
Authors: Yu Morozova G
Published: November 2021

The results of a comparative analysis of the vitality structure of Acer negundo populations during ontogenetic development in an urban environment are presented. The vitality structure of A. negundo populations is changing from prosperous to depressive, with the changing living condition of individuals and the quality of populations in urban conditions. The quality index of A negundo populations was in the amplitude from 0.5 to 0.166 along the urbanization gradient. High plasticity and variability of A negundo in combination with the dynamic vitality structure on the background of anthropogenic impacts provide active colonization of this invasive species in the city.
State of Cenopopulations of Trommsdorffia ciliata (Thunb.) H.S. Pak (Asteraceae) in the Plant Communities of the Lower Reaches of the Ussuri River
Authors: Motorykina T N
Published: November 2021

The paper presents the results of studying the structure and state of four cenopopulations of the rare species Trommsdorffia ciliata (Thunb.) H.S. Pak in the valley of the lower reaches of the Ussuri River. The density of the studied cenopopulations is from 8 to 27 ind./m2. All studied cenopopulations are normal and incomplete. The absence or small number of juveniles in the ontogenetic spectrum of the studied cenopopulations is associated with a high projective cover of the herbaceous layer, which prevents the survival of this age group. According to the absolute maximum of ontogenetic groups of adult plants of all cenopopulations, Trommsdorffia ciliata are classified as young normal ones, where the maximum falls on individuals of the virginal state. An evaluation of population and organismic signs of the state of the studied cenopopulations showed that the most favorable conditions for the growth of Trommsdorffia ciliata are formed in a moist sedge-grass-herb meadow in the vicinity of Lonchakovo village. The measures for the protection of Trommsdorffia ciliata that are to include in the Red Book of the Khabarovsk krai (2019), to inhabit in a protected area and are to control the state of the known population of this species have been cited.
International key ornithological areas of the Khabarovsk Territory
Authors: Pronkevich V V
Published: November 2021

A list of key areas of the Khabarovsk Territory, which are of international importance for the conservation of bird populations, is provided on the basis of our own data and academic sources. A brief description of the ornithological significance and the conservation status of 19 areas are presented. The major factors determining the formation of increased densities of breeding birds and mass gatherings of migrants are considered. Twelve species are used as identifiers for International Key Bird Areas. They are represented by the following families: Phalacrocoracidae (1 species), Anatidae (2), Accipitridae (1), Scolopacidae (1), Laridae (1), and Alcidae (6). Among the 19 areas important for birds, 7 areas have a conservation status. Other areas either do not have a protected status, or it covers only a part of important habitats. Information is provided on the prospects for the organization of protected areas in some sea bays of the Sea of Okhotsk.
Spatial distinction analysis on marine ranch development potential in coastal areas of China
Authors: Xu Sh , Gao Y , Li F , Cheng H , Liu Q
Published: November 2021

According to the 14th Five-Year Plan and the outline of 2035 long-term goals, a modern marine industrial system should be built, the layout of green offshore aquaculture should be optimized, and marine ranching should be built. The research on the construction of marine ranching can provide new ideas for sustainable ecological fishery and inject new vitality into the development of marine industry. In the future, the construction of marine ranching will be a vast world. In this paper, from the perspective of geography, the GC-TOPSIS method combined with the entropy weight TOPSIS method and the grey correlation method were used to construct 22 evaluation index systems to estimate the development potential of marine ranching construction in ten coastal provinces and municipalities of China from 2011 to 2016. The results showed that the overall development potential of marine ranching in ten provinces and urban areas had regional differences (north, central and south), and the differences in the north and south regions were obvious. The regional differences in the central coastal areas of China were not significant, and the development potentials of marine ranching in ten provinces and urban areas were all medium. The development potential of four criteria layers of marine ranching in ten coastal provinces and regions of China is different in space, and the development potential of marine ranching in the same region is unbalanced in all aspects of the criteria layers. To estimate the development potential of marine ranching in China’s ten coastal provinces and regions provides scientific support for the sustainable development of ecological fisheries, and has practical application value for the scientific planning of marine ranching and the selection of demonstration areas.
Experimental investigation and parameters optimization on jet electrochemical machining to improve the surface performance of additive-manufactured 316L stainless steel parts
Authors: Cheng Haixia , Lou Guibin , Shen Lida , Zhang Ming , Yang Youwen , Xie Deqiao , Chen Ya , Bai Huawen , Tian Zongjun , Zhao Jianfeng
Published: November 2021

For metal parts, selective laser melting (SLM) technology has obvious advantages over traditional forming methods. Parts manufactured by selective laser melting are abbreviated as SLMed Parts. However, the surfaces of SLMed parts have many defects such as adhered particles and pores. These defects lead to poor surface quality of the parts, thus restricting the promotion of SLM technology. Therefore, the paper uses jet electrochemical machining (JECM) to remove the surface defects of SLMed sample. Optimization is technique used in manufacturing sectors to generate the best manufacturing conditions. There are many process variables involved in the JECM process, and it is difficult to select an appropriate parameters combination to maximize the removal of surface defects while minimizing material removal thickness and surface roughness. The purpose of this work is to study the influence of process parameters such as electrolyte temperature, processing time, and current density on material removal thickness, surface roughness and material removal rate in the JECM process. In Minitab19, the L25 made by Taguchi orthogonal array was used in the experiment. Each experiment is carried out under different input parameters, and the data were analyzed through analysis of variance (ANOVA). The optimized processing parameters associated with performance parameters are given and ultimately the experimental results were verified.
Differentiation between normal and tumor mammary glands with depth-resolved attenuation coefficient from optical coherence tomography
Authors: Maciel Marino J , Pereira Hugo M , Pimenta Sara , Miranda Alice , Nunes-Pereira Eduardo J , Correia José H
Published: November 2021

Optical coherence tomography (OCT) is a well-established imaging technology for high-resolution, cross-sectional imaging of biological tissues. Imaging processing and light attenuation coefficient estimation allows to further improve the OCT diagnostic capability. In this paper we use a commercial OCT system, Telesto II-1325LR from Thorlabs, and demonstrate its ability to differentiate normal and tumor mammary mouse glands with the OCT attenuation coefficient. Using several OCT images of normal and tumor mammary mouse glands (n = 26), a statistical analysis was performed. The attenuation coefficient was calculated in depth, considering a slope of 0.5 mm. The normal glands present a median attenuation coefficient of 0.403 mm−1, comparatively to 0.561 mm−1 obtained for tumor mammary glands. This translates in an attenuation coefficient approximately 39% higher for tumor mammary glands when compared to normal mammary glands. The OCT attenuation coefficient estimation eliminates the subjective analysis provided by direct visualization of the OCT images.
Design of improved compact decoupler based on adjustable capacitor for EAST-ICRF antenna
Authors: CHEN Gen , MAO Yuzhou , YUAN Shuai , ZHAO Yanping , YANG Hua , ZHANG Xinjun , QIN Chengming , CHENG Yan , WANG Yongsheng
Published: November 2021

The Ion Cyclotron Radio Frequency (ICRF) heating antenna on EAST adopts a decoupling device to constrain power coupling among the radiation straps, which was discovered shortcomings such as long size, poor contact, and etc. In order to improve these weak points, a new type decoupler with terminal-loaded tunable capacitor is designed to replace the previous design. Besides the capability of the tunable admittance parameters of decoupler, the withstand voltage of the capacitor is the most significant consideration for working under high power. Therefore, the theoretical analysis carefully elaborates the capacitor withstand voltage, and the detailed analytical equations and criteria for design are given. After the comparative analysis of theoretical calculation and 3D simulation results, the decoupler design scheme is finalized. The capacitor-loaded decoupler has been successfully adopted for ICRF antenna at port N on EAST, and achieved the optimization of adjacent port isolation from −22 to −58 dB at 37 MHz without plasma to restrict mutual coupling. The new design of the decoupler has greatly improved its compactness and automatic adjustment performance, and could be good solution for the decoupling network of ICRF antennas.
Enhanced discrimination of high-dimensional quantum states by concatenated optimal measurement strategies
Authors: Solís-Prosser M A , Jiménez O , Delgado A , Neves L
Published: November 2021

The impossibility of deterministic and error-free discrimination among nonorthogonal quantum states lies at the core of quantum theory and constitutes a primitive for secure quantum communication. Demanding determinism leads to errors, while demanding certainty leads to some inconclusiveness. One of the most fundamental strategies developed for this task is the optimal unambiguous measurement. It encompasses conclusive results, which allow for error-free state retrodictions with the maximum success probability, and inconclusive results, which are discarded for not allowing perfect identifications. Interestingly, in high-dimensional Hilbert spaces the inconclusive results may contain valuable information about the input states. Here, we theoretically describe and experimentally demonstrate the discrimination of nonorthogonal states from both conclusive and inconclusive results in the optimal unambiguous strategy, by concatenating a minimum-error measurement at its inconclusive space. Our implementation comprises four- and nine-dimensional spatially encoded photonic states. By accessing the inconclusive space to retrieve the information that is wasted in the conventional protocol, we achieve significant increases of up to a factor of 2.07 and 3.73, respectively, in the overall probabilities of correct retrodictions. The concept of concatenated optimal measurements demonstrated here can be extended to other strategies and will enable one to explore the full potential of high-dimensional nonorthogonal states for quantum communication with larger alphabets.
Analyzing the impacts of land use policies on selected ecosystem services in the upper Chattahoochee Watershed, Georgia, United States
Authors: Benez-Secanho Fabio Jose , Dwivedi Puneet
Published: November 2021

The rapid rate of urbanization within the Upper Chattahoochee Watershed (UCW) is threatening the provision of ecosystem services (ESs) for six million residents of the Atlanta Metropolitan Area. This study uses the land cover change model TerrSet to project future land cover from 2016 to 2040. The modular toolset InVEST (Integrated Valuation of Ecosystem Services and Tradeoffs) is used to assess the efficacy of four land use policies in maintaining the provision of three ESs (carbon storage, wildlife habitat, and water quality) within the UCW. The Baseline scenario represents past urbanization trends, whereas the Urbanization scenario accounts for a higher urban growth rate. The Plan 2040 scenario includes existing policy guidelines, and the Conservation scenario adds forested riparian buffer areas. Two integrated indexes and an economic valuation of ESs were used to combine all ESs and analyze the overall performance of each policy. The first index uses unequal weights for ESs based on the Analytical Hierarchical Process, whereas the second index uses equal weights. The values of both integrated indexes and economic values were highest in the Conservation scenario and lowest in the Urbanization scenario. No significant differences in the provision of ESs were found between the Baseline and the Plan 2040 scenarios. However, the integrated indexes and economic values for both land use policies declined over time. Our study will feed into the ongoing movement of sustainable watershed management for ensuring the provision of ESs, especially for rapidly urbanizing cities worldwide, in general, and in the United States, in particular.
Increasing spring dust storms in the future over the Taklimakan Desert, Northwest China: implications from changes in circulation pattern frequency in CMIP6
Authors: Mao Rui , Gong Dao-Yi , Kim Seong-Joong , Zong Qi , Feng Xingya , Zhang Xiao-Xiao
Published: November 2021

Dust storms over the Taklimakan Desert (TD), Northwest China, not only influence human health but also affect regional climate through direct effects of dust aerosols on solar and longwave radiation. The Coupled Model Intercomparisons Project Phase 5 (CMIP5) models project a decrease in dust storms because of a decrease in dust emissions over the TD in the future under warming scenarios. However, inaccurate simulations of dust emissions cause the CMIP5 models to simulate dust storms poorly. Here we analyzed typical circulation patterns that initiate dust storms over the TD and examined changes in the frequency of typical circulation patterns derived from the CMIP6 models in an extreme warming scenario. The results show that there will be an increase in typical circulation pattern frequency in the latter half of the 21st century compared with 1958–2014, implying an increase in dust storms over the TD in the future under the extreme warming scenario. The increase in dust storms over the TD may be related to an increase in synoptic activities in the future from the Middle Asia to the TD, which is caused by a southern movement of subtropical westerly jet stream under the extreme warming scenario.
Nanosecond laser shock detonation of nanodiamonds: from laser-matter interaction to graphite-to-diamond phase transition
Authors: Zhang Xing , Sun Haofan , Mao Bo , Dai Rui , Zhuang Houlong , Liao Yiliang , Nian Qiong
Published: November 2021

Nanodiamonds (NDs) have been widely explored for applications in drug delivery, optical bioimaging, sensors, quantum computing, and others. Room-temperature nanomanufacturing of NDs in open air using confined laser shock detonation (CLSD) emerges as a novel manufacturing strategy for ND fabrication. However, the fundamental process mechanism remains unclear. This work investigates the underlying mechanisms responsible for nanomanufacturing of NDs during CLSD with a focus on the laser-matter interaction, the role of the confining effect, and the graphite-to-diamond transition. Specifically, a first-principles model is integrated with a molecular dynamics simulation to describe the laser-induced thermo-hydrodynamic phenomena and the graphite-to-diamond phase transition during CLSD. The simulation results elucidate the confining effect in determining the material’s responses to laser irradiation in terms of the temporal and spatial evolutions of temperature, pressure, electron number density, and particle velocity. The integrated model demonstrates the capability of predicting the laser energy threshold for ND synthesis and the efficiency of ND nucleation under varying processing parameters. This research will provide significant insights into CLSD and advance this nanomanufacturing strategy for the fabrication of NDs and other high-temperature-high-pressure synthesized nanomaterials towards extensive applications.
On the solidification of the manifold of the t-distributed stochastic neighbour embedding for condition classification of machine tools
Authors: Wang Jing , Cheng Xiaobin , Wang Xun , Gao Yan , Liu Bin , Han Mingmei , Yang Jun
Published: November 2021

t-distributed stochastic neighbour embedding (t-SNE) is of considerable interest in machining condition monitoring for feature selection. In this paper, the neural networks are introduced to solidify the manifold of the t-SNE prior to classification. This leads to the improved feature selection method, namely the Net-SNE. Conventional statistical features are first extracted from vibration signals to form a high dimensional feature vector. The redundancies in the feature vector are subsequently removed by the t-SNE. Then the neural networks build a mapping model between the high dimensional feature vector and the selected features. The new data is calculated directly using the mapping model. The experiments were conducted on a lathe and a milling machine to collect vibration signals under common working conditions. The K-nearest neighbour classifier is applied to a small sample case and a class-imbalance case to compare the classification performance with and without the Net-SNE. The results demonstrate that the Net-SNE has the advantage over the t-SNE, since it can mine the discriminative features and solidifiy the manifold in the calculation of the new data. Moreover, the proposed method significantly improves the classification accuracy by Net-SNE, along with better classification performance in data-limited situations.
High-Resolution Ultrasound-Assisted Assessment of Preliminary Short-term Safety Outcomes of an Implant-Based Augmentation Mammaplasty Using a Bioengineered, Cell-Friendly, Smooth-Surface Device in Korean Females
Authors: Lee Sangdal , Jeong Jeong Pil , Sung Jung Youp , Choi Woo Sik , Moon Dong Seung , Kim Ho Chan , Kim Jae Hong
Published: November 2021

Background

The Motiva Ergonomix Round SilkSurface (Establishment Labs Holdings Inc., Alajuela, Costa Rica) is one of the representative brands of the fifth generation of a silicone gel-filled breast implant with a microtextured surface.

Objectives

In this study, the authors describe preliminary short-term safety outcomes of an implant-based augmentation mammaplasty using the Motiva Ergonomix Round SilkSurface in Korean females.

Methods

The authors performed a retrospective analysis of medical records in a total of 69 females (n = 69) receiving an implant-based augmentation mammaplasty using the Motiva Ergonomix Round SilkSurface between September 26, 2017, and December 31, 2020. The authors analyzed incidences of postoperative complications.

Results

A total of 6 cases (8.7%) of postoperative complications occurred; these include 2 cases (2.9%) of early seroma, 1 case (1.4%) of capsular contracture, 2 cases (2.9%) of alterations in the shape, and 1 case (1.4%) of foreign body sensation. Time-to-events were estimated at 266.81 ± 273.17 days.

Conclusions

The authors describe our preliminary short-term safety outcomes of an implant-based augmentation mammaplasty using the Motiva Ergonomix Round SilkSurface in Korean females. But this deserves further large-scale studies with long periods of follow-up.

Level of Evidence: 4
A deep learning model to identify gene expression level using cobinding transcription factor signals
Authors: Zhang Lirong , Yang Yanchao , Chai Lu , Li Qianzhong , Liu Junjie , Lin Hao , Liu Li
Published: November 2021

Gene expression is directly controlled by transcription factors (TFs) in a complex combination manner. It remains a challenging task to systematically infer how the cooperative binding of TFs drives gene activity. Here, we quantitatively analyzed the correlation between TFs and surveyed the TF interaction networks associated with gene expression in GM12878 and K562 cell lines. We identified six TF modules associated with gene expression in each cell line. Furthermore, according to the enrichment characteristics of TFs in these TF modules around a target gene, a convolutional neural network model, called TFCNN, was constructed to identify gene expression level. Results showed that the TFCNN model achieved a good prediction performance for gene expression. The average of the area under receiver operating characteristics curve (AUC) can reach up to 0.975 and 0.976, respectively in GM12878 and K562 cell lines. By comparison, we found that the TFCNN model outperformed the prediction models based on SVM and LDA. This is due to the TFCNN model could better extract the combinatorial interaction among TFs. Further analysis indicated that the abundant binding of regulatory TFs dominates expression of target genes, while the cooperative interaction between TFs has a subtle regulatory effects. And gene expression could be regulated by different TF combinations in a nonlinear way. These results are helpful for deciphering the mechanism of TF combination regulating gene expression.
Magnetic resonance reveals mitochondrial dysfunction and muscle remodelling in spinal muscular atrophy
Authors: Habets Laura E , Bartels Bart , Asselman Fay-Lynn , Hooijmans Melissa T , van den Berg Sandra , Nederveen Aart J , van der Pol W Ludo , Jeneson Jeroen A L
Published: November 2021

Genetic therapy has changed the prognosis of hereditary proximal spinal muscular atrophy, although treatment efficacy has been variable. There is a clear need for deeper understanding of underlying causes of muscle weakness and exercise intolerance in patients with this disease to further optimize treatment strategies. Animal models suggest that in addition to motor neuron and associated musculature degeneration, intrinsic abnormalities of muscle itself including mitochondrial dysfunction contribute to the disease aetiology.

To test this hypothesis in patients, we conducted the first in vivo clinical investigation of muscle bioenergetics. We recruited 15 patients and 15 healthy age and gender-matched control subjects in this cross-sectional clinico-radiological study. MRI and 31P magnetic resonance spectroscopy, the modality of choice to interrogate muscle energetics and phenotypic fibre-type makeup, was performed of the proximal arm musculature in combination with fatiguing arm-cycling exercise and blood lactate testing. We derived bioenergetic parameter estimates including: blood lactate, intramuscular pH and inorganic phosphate accumulation during exercise, and muscle dynamic recovery constants. A linear correlation was used to test for associations between muscle morphological and bioenergetic parameters and clinico-functional measures of muscle weakness.

MRI showed significant atrophy of triceps but not biceps muscles in patients. Maximal voluntary contraction force normalized to muscle cross-sectional area for both arm muscles was 1.4-fold lower in patients than in controls, indicating altered intrinsic muscle properties other than atrophy contributed to muscle weakness in this cohort. In vivo31P magnetic resonance spectroscopy identified white-to-red remodelling of residual proximal arm musculature in patients on the basis of altered intramuscular inorganic phosphate accumulation during arm-cycling in red versus white and intermediate myofibres. Blood lactate rise during arm-cycling was blunted in patients and correlated with muscle weakness and phenotypic muscle makeup. Post-exercise metabolic recovery was slower in residual intramuscular white myofibres in patients demonstrating mitochondrial ATP synthetic dysfunction in this particular fibre type.

This study provides the first in vivo evidence in patients that degeneration of motor neurons and associated musculature causing atrophy and muscle weakness in 5q spinal muscular atrophy type 3 and 4 is aggravated by disproportionate depletion of myofibres that contract fastest and strongest. Our finding of decreased mitochondrial ATP synthetic function selectively in residual white myofibres provides both a possible clue to understanding the apparent vulnerability of this particular fibre type in 5q spinal muscular atrophy types 3 and 4 as well as a new biomarker and target for therapy.
Neuroanatomical anomalies associated with rareAP4E1mutations in people who stutter
Authors: Chow Ho Ming , Li Hua , Liu Siyuan , Frigerio-Domingues Carlos , Drayna Dennis
Published: November 2021

Developmental stuttering is a common speech disorder with strong genetic underpinnings. Recently, stuttering has been associated with mutations in genes involved in lysosomal enzyme trafficking. However, how these mutations affect the brains of people who stutter remains largely unknown. In this study, we compared grey matter volume and white matter fractional anisotropy between a unique group of seven subjects who stutter and carry the same rare heterozygous AP4E1 coding mutations and seven unrelated controls without such variants. The carriers of the AP4E1 mutations are members of a large Cameroonian family in which the association between AP4E1 and persistent stuttering was previously identified. Compared to controls, mutation carriers showed reduced grey matter volume in the thalamus, visual areas and the posterior cingulate cortex. Moreover, reduced fractional anisotropy was observed in the corpus callosum, consistent with the results of previous neuroimaging studies of people who stutter with unknown genetic backgrounds. Analysis of gene expression data showed that these structural differences appeared at the locations in which expression of AP4E1 is relatively high. Moreover, the pattern of grey matter volume differences was significantly associated with AP4E1 expression across the left supratentorial regions. This spatial congruency further supports the connection between AP4E1 mutations and the observed structural differences.
Extracellular histones, a new class of inhibitory molecules of CNS axonal regeneration
Authors: Siddiq Mustafa M , Hannila Sari S , Zorina Yana , Nikulina Elena , Rabinovich Vera , Hou Jianwei , Huq Rumana , Richman Erica L , Tolentino Rosa E , Hansen Jens , Velenosi Adam , Kwon Brian K , Tsirka Stella E , Maze Ian , Sebra Robert , Beaumont Kristin G , Toro Carlos A , Cardozo Christopher P , Iyengar Ravi , Filbin Marie T
Published: November 2021

Axonal regeneration in the mature CNS is limited by extracellular inhibitory factors. Triple knockout mice lacking the major myelin-associated inhibitors do not display spontaneous regeneration after injury, indicating the presence of other inhibitors. Searching for such inhibitors, we have detected elevated levels of histone H3 in human CSF 24 h after spinal cord injury. Following dorsal column lesions in mice and optic nerve crushes in rats, elevated levels of extracellular histone H3 were detected at the injury site. Similar to myelin-associated inhibitors, these extracellular histones induced growth cone collapse and inhibited neurite outgrowth. Histones mediate inhibition through the transcription factor Y-box-binding protein 1 and Toll-like receptor 2, and these effects are independent of the Nogo receptor. Histone-mediated inhibition can be reversed by the addition of activated protein C in vitro, and activated protein C treatment promotes axonal regeneration in the crushed optic nerve in vivo. These findings identify extracellular histones as a new class of nerve regeneration-inhibiting molecules within the injured CNS.
Passive localization of the central sulcus during sleep based on intracranial EEG
Authors: Alkawadri Rafeed , Zaveri Hitten P , Sheth Kevin N , Spencer Dennis D
Published: November 2021

We test the performance of a novel operator-independent EEG-based method for passive identification of the central sulcus (CS) and sensorimotor (SM) cortex. We studied seven patients with intractable epilepsy undergoing intracranial EEG (icEEG) monitoring, in whom CS localization was accomplished by standard methods. Our innovative approach takes advantage of intrinsic properties of the primary motor cortex (MC), which exhibits enhanced icEEG band-power and coherence across the CS. For each contact, we computed a composite power, coherence, and entropy values for activity in the high gamma band (80–115) Hz of 6–10 min of NREM sleep. Statistically transformed EEG data values that did not reach a threshold (th) were set to 0. We computed a metric M based on the transformed values and the mean Euclidian distance of each contact from contacts with Z-scores higher than 0. The last step was implemented to accentuate local network activity. The SM cortex exhibited higher EEG-band-power than non-SM cortex (P < 0.0002). There was no significant difference between the motor/premotor and sensory cortices (P < 0.47). CS was localized in all patients with 0.4 < th < 0.6. The primary hand and leg motor areas showed the highest metric values followed by the tongue motor area. Higher threshold values were specific (94%) for the anterior bank of the CS but not sensitive (42%). Intermediate threshold values achieved an acceptable trade-off (0.4: 89% specific and 70% sensitive).
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure
Authors: Wu Jing , Zhao Min , Li Tao , Sun Jinxiu , Chen Qi , Yin Chengliang , Jia Zhilong , Zhao Chenghui , Lin Gui , Ni Yuan , Xie Guotong , Shi Jinlong , He Kunlun
Published: November 2021

As the terminal clinical phenotype of almost all types of cardiovascular diseases, heart failure (HF) is a complex and heterogeneous syndrome leading to considerable morbidity and mortality. Existing HF-related omics studies mainly focus on case/control comparisons, small cohorts of special subtypes, etc., and a large amount of multi-omics data and knowledge have been generated. However, it is difficult for researchers to obtain biological and clinical insights from these scattered data and knowledge. In this paper, we built the Heart Failure Integrated Platform (HFIP) for data exploration, fusion analysis and visualization by collecting and curating existing multi-omics data and knowledge from various public sources and also provided an auto-updating mechanism for future integration. The developed HFIP contained 253 datasets (7842 samples), multiple analysis flow, and 14 independent tools. In addition, based on the integration of existing databases and literature, a knowledge base for HF was constructed with a scoring system for evaluating the relationship between molecular signals and HF. The knowledge base includes 1956 genes and annotation information. The literature mining module was developed to assist the researcher to overview the hotspots and contexts in basic and clinical research. HFIP can be used as a data-driven and knowledge-guided platform for the basic and clinical research of HF.

Database URL: http://heartfailure.medical-bigdata.com
Death, sex, and fertility: female infanticide in rural Spain, 1750–1950
Authors: Beltrán Tapia Francisco J , Marco-Gracia Francisco J
Published: November 2021

Relying on longitudinal micro data from rural Spain between 1750 and 1950, this article evidences that families mortally neglected a significant fraction of their female babies. Firstly, baptism records exhibited exceptionally high sex ratios at birth until the late nineteenth century. Secondly, having no previous male siblings increased the probability of male baptisms. Likewise, this same feature, together with the number of siblings alive, also increased female mortality during the first day of life. These findings are concentrated at higher parities and among landless and semi-landless families. Lastly, under-registration cannot explain these patterns affecting female mortality shortly after birth.
Miniseries 1—Part II: the comparative anatomy of the atrioventricular conduction axis
Authors: Macías Yolanda , de Almeida Marcos C , Tretter Justin T , Anderson Robert H , Spicer Diane E , Mohun Timothy J , Sánchez-Quintana Damián , Farré Jerónimo , Back Sternick Eduardo
Published: November 2021

Aims

The arrangement of the conduction axis is markedly different in various mammalian species. Knowledge of such variation may serve to question the validity of using animals as prospective models for design of systems for clinical use.

Methods and results

We compared the arrangement of the atrioventricular conduction axis in human, murine, canine, porcine, and bovine hearts, examining serially sectioned datasets from 20 human, 16 murine, 3 porcine, 5 canine, and 1 bovine hearts. We also analysed computed tomographic datasets obtained from bovines and one human heart. Unlike the situation in the human heart, there is no formation of an atrioventricular fibrous membranous septum in the murine, canine, porcine, nor bovine hearts. Canine, porcine, and bovine hearts also lack an infero-septal recess, when defined as a fibrous plate supporting the buttress of the atrial septum. In these species, half of the non-coronary leaflet is directly opposed to the ventricular septal surface.

Conclusion

There is a long right-sided non-branching component of the axis, which skirts the attachment of the non-coronary sinus of the aortic root. In the bovine heart, moreover, the left bundle branch usually extends intramyocardially as a solitary tape before surfacing and ramifying on the left ventricular septal surface. The difference in the atrioventricular conduction axis between species may influence the anatomical substrates for atrioventricular re-entry tachycardia, as well as providing inferences for assessing the risks of transcatheter implantation of the aortic valve. Further studies are now needed to assess these possibilities.
Miniseries 2—Septal and paraseptal accessory pathways—Part I: The anatomic basis for the understanding of para-Hisian accessory atrioventricular pathways
Authors: Anderson Robert H , Sanchez-Quintana Damian , Mori Shumpei , Spicer Diane E , Wellens Hein J J , Lokhwandala Yash , Cabrera Jose-Angel , Farre Jeronimo , Sternick Eduardo Back
Published: November 2021

Aims

Although the anatomy of the atrioventricular conduction axis was well described over a century ago, the precise arrangement in the regions surrounding its transition from the atrioventricular node to the so-called bundle of His remain uncertain. We aimed to clarify these relationships.

Methods and results

We have used our various datasets to examine the development and anatomical arrangement of the atrioventricular conduction axis, paying particular attention to the regions surrounding the point of penetration of the bundle of His. It is the areas directly adjacent to the transition of the atrioventricular conduction axis from the atrioventricular node to the non-branching atrioventricular bundle that constitute the para-Hisian areas. The atrioventricular conduction axis itself traverses the membranous part of the ventricular septum as it extends from the node to become the bundle, but the para-Hisian areas themselves are paraseptal. This is because they incorporate the fibrofatty tissues of the inferior pyramidal space and the superior atrioventricular groove. In this initial overarching review, we summarize the developmental and anatomical features of these areas along with the location and landmarks of the atrioventricular conduction axis. We emphasize the relationships between the inferior pyramidal space and the infero-septal recess of the subaortic outflow tract. The details are then explored in greater detail in the additional reviews provided within our miniseries.

Conclusion

Our anatomical findings, described here, provide the basis for our concomitant clinical review of the so-called para-Hisian arrhythmias. The findings also provide the basis for understanding the other variants of ventricular pre-excitation.
Light Intervention Effects on Circadian Activity Rhythm Parameters and Nighttime Sleep in Dementia Assessed by Wrist Actigraphy: A Systematic Review and Meta-Analysis
Authors: Canazei Markus , Papousek Ilona , Weiss Elisabeth M
Published: November 2021

Background and Objectives

Persons with dementia often show circadian rhythm disturbances and sleep problems. Timed light exposure seems to be a promising nonpharmacological treatment option. In this review, meta-analyses were run on light effects on circadian activity rhythm parameters in persons with dementia measured with wrist actimetry. Furthermore, we update a Cochrane review, published in 2014, on actigraphically measured light effects in nighttime sleep parameters in persons with dementia.

Research Design and Methods

Four electronic databases were searched for randomized controlled trials. Effects in meta-analyses were summarized by using mean differences and 95% confidence intervals. We followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to assess the risk of bias and registered the review protocol (PROSPERO: CRD42020149001).

Results

Thirteen trials met inclusion criteria, and either utilized light therapy devices, ambient room lighting systems, or dawn–dusk interventions. Eleven of these studies were subjected to meta-analyses. They did not reveal significant light effects on circadian activity parameters: amplitude (p = .62; n = 313), acrophase (p = .34; n = 313), intradaily variability (p = .51; n = 354), and interdaily stability (p = .38; n = 354). Furthermore, no light effects were found on sleep parameters: total sleep duration (p = .53; n = 594), sleep efficiency (p = .63; n = 333), wake after sleep onset (p = .95; n = 212), and sleep onset latency (p = .26; n = 156). Subgroup analyses, pooling data from 3 studies including persons with Alzheimer’s dementia, also did not show light effects on circadian activity and sleep parameters. The overall risk of bias of included studies was high.

Discussion and Implications

There is insufficient evidence for actigraphically measured circadian light effects in persons with dementia. More high-quality research is needed to recommend the application of adjunctive light.