bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation and prediction of three-dimensional rotating flows based on convolutional neural networks
Authors: Gao Feng , Zhang Zhuang , Jia Chenyang , Zhu Yin , Zhou Chunli , Wang Jingtao
Published: August 2022

Two deep learning models to reconstruct three-dimensional (3D) steady-state rotating flows are proposed to capture the spatial information: the 3D convolutional encoder–decoder and the 3D convolutional long short-term memory model. They are based on deep learning methods such as the encoder–decoder convolutional neural network and recurrent neural network. Their common components are an encoder, a middle layer, and a decoder. The rotating flows in a stirred tank with four inclined blades are calculated for the dataset to train and test the two models. A workflow for the flow field reconstruction is established and all variants made up of various components are executed according to the flow. The optimal networks of the two models are selected by comparing performance measures. The results show that both models have the excellent ability to fit the 3D rotating flow field. Performance measures of the second model are better than those of the first one, but its running time is slower than that of the first one. In practice, this method can be used in the design and optimization of stirred tanks, centrifugal pumps, and other machines with rotating parts.
Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells
Authors: Liu Wen-Yu , Yu Chun-Ping , Chang Chao-Kang , Chen Hsiang-June , Li Meng-Yun , Chen Yi-Hua , Shiu Shin-Han , Ku Maurice S. B. , Tu Shih-Long , Lu Mei-Yeh Jade , Li Wen-Hsiung
Published: August 2022

The superior photosynthetic efficiency of C4leaves over C3leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.
Relative calibration of the LIGO and Virgo detectors using astrophysical events from their third observing run
Authors: Alléné C , Andres N , Assiduo M , Aubin F , Buskulic D , Chierici R , Estevez D , Faedi F , Guidi G M , Juste V , Marion F , Mours B , Nitoglia E , Sordini V , Syx A
Published: August 2022

We explore a method to assess the relative scale of the strain measured in the different detectors of the gravitational-wave (GW) network, using binary black hole (BBH) events detected during the third observing run (O3). The number of such signals is becoming sufficiently large to adopt a statistical approach based on the ratio of the signal-to-noise ratio of the events between the detectors and the number of observed events in each detector. We demonstrate the principle of the method on simulations of BBH signals and we present its application to published O3 events reported by the multi-band template analysis pipeline. Constraints on the relative calibration of the GW network for O3 are obtained at the level of

∼
3.5
%

between the two LIGO detectors and at the level of

∼
10
%

between the LIGO Livingston detector and the Virgo detector.
Enhancement of frequency scanning interferometry signal for non-cooperative target based on generative adversarial network
Authors: Tian Kai , Liu Zhigang , Zhang Huakun , Wang Zian , Guo Junkang
Published: August 2022

In non-cooperative target frequency scanning interferometry, the return optical power is low, the quality of the interferometric signal is poor, and the signal-to-noise ratio (SNR) is low. Moreover, the power change accompanying the use of the frequency scanning laser modulates the interferometric signal’s amplitude and shifts the amplitude centre. Traditional signal enhancement techniques, such as filtering, can only solve some of the problems affecting the measurement accuracy, and the full-factor processing of such signals is difficult. This paper proposes a non-cooperative target frequency scanning interferometry signal enhancement method based on a generative adversarial network. By learning the sample dataset, the SNR of the signal can be improved within a certain range, and the signal waveform can be corrected simultaneously. The simulation results reveal that the SNR of the non-cooperative target signal is improved and the signal waveform is satisfactorily corrected. Finally, the effectiveness of the enhancement method was experimentally confirmed.
Noise analysis of MoTe2-based dual-cavity MOSFET as a pH sensor
Authors: De Arpan , Kanrar Sharmistha Shee , Sarkar Subir Kumar
Published: August 2022

Field-effect transistor (FET) pH sensors have been studied for a long time because of their low cost, sound sensitivity, and high operational speed. Recently, transition metal dichalcogenides (TMD) materials such as MoTe2, MoS2, among others, have emerged as promising channel materials for developing energy-efficient electronic devices. TMD-based sensors have shown excellent results because of the high surface area–volume ratio and better bio-specific interaction. This paper proposes and analyzes a MoTe2 channel–based dual-cavity (DC) accumulation metal oxide semiconductor field effect transistor (MOSFET) as a pH sensor. For a comprehensive study, a pH-FET noise model has been considered to investigate the amount of noise associated with the proposed FET under various ionic concentrations and device dimensions. The electrolytic semiconductor has been modeled based on ion dynamics for the simulation study. A site-binding model has been incorporated to capture the surface charge density fluctuations at the interface of electrolyte and gate oxide for different pH values. The effect of gate length scaling on the device performance is studied to comprehend its scalability. With this MoTe2-based DC accumulation MOSFET sensor, a peak threshold sensitivity of 77 mV pH−1 has been achieved. To provide a comparative performance analysis of the proposed work, a benchmarking figure is included and a detailed fabrication methodology is also presented in this paper. All simulations are performed with an experimentally calibrated setup in SILVACO Technology Computer Aided Design (TCAD).
Induced gravitational waves from multi-sound speed resonances during cosmological inflation
Authors: Addazi Andrea , Capozziello Salvatore , Gan Qingyu
Published: August 2022

We explore the possibility of multi-parametric resonances from time varying sound speed during cosmological inflation. In particular, we fix our set-up to the simpler case beyond a single oscillation model already explored in literature: two sinusoidal harmonics around a constant sound speed equal to one. We find that, within the perturbative regime, except for some certain extreme corners of the parameter space, the primordial density spectrum is characterized by two groups of amplified peaks centered around two critical oscillatory frequencies of the sound speed. As a general result, we show that the energy spectrum of the secondary induced GWs from the inflationary era has a single major broad peak, whereas the one from the radiation dominated phase consists of one/two principle peak-like configuration(s) for relatively small/large ratio of two oscillatory frequencies. The GW relic stochastic backgrounds carry a gravitational memory of the parametric resonances during inflation. GW signals from double sound speed resonances can be tested in complementary channels from Pulsar-timing radio-astronomy, space and terrestrial GW interferometers.
Artificial referred sensation in upper and lower limb prosthesis users: a systematic review
Authors: Gonzalez Michael , Bismuth Alex , Lee Christina , Chestek Cynthia A , Gates Deanna H
Published: August 2022

Objective. Electrical stimulation can induce sensation in the phantom limb of individuals with amputation. It is difficult to generalize existing findings as there are many approaches to delivering stimulation and to assessing the characteristics and benefits of sensation. Therefore, the goal of this systematic review was to explore the stimulation parameters that effectively elicited referred sensation, the qualities of elicited sensation, and how the utility of referred sensation was assessed. Approach. We searched PubMed, Web of Science, and Engineering Village through January of 2022 to identify relevant papers. We included papers which electrically induced referred sensation in individuals with limb loss and excluded papers that did not contain stimulation parameters or outcome measures pertaining to stimulation. We extracted information on participant demographics, stimulation approaches, and participant outcomes. Main results. After applying exclusion criteria, 49 papers were included covering nine stimulation methods. Amplitude was the most commonly adjusted parameter (n = 25), followed by frequency (n = 22), and pulse width (n = 15). Of the 63 reports of sensation quality, most reported feelings of pressure (n = 52), paresthesia (n = 48), or vibration (n = 40) while less than half (n = 29) reported a sense of position or movement. Most papers evaluated the functional benefits of sensation (n = 33) using force matching or object identification tasks, while fewer papers quantified subjective measures (n = 16) such as pain or embodiment. Only 15 studies (36%) observed percept intensity, quality, or location over multiple sessions. Significance. Most studies that measured functional performance demonstrated some benefit to providing participants with sensory feedback. However, few studies could experimentally manipulate sensation location or quality. Direct comparisons between studies were limited by variability in methodologies and outcome measures. As such, we offer recommendations to aid in more standardized reporting for future research.
Magnetic system for controlling the spin of polarized neutrons
Authors: Berikov D. , Ahmadov G. , Kopatch Yu. , Novitsky V.
Published: August 2022

A spin control magnetic system was developed and assembled
at the JINR Laboratory of Neutron Physics (Dubna, Russia) and was
tested with a beam of polarized neutrons at the POLI instrument of
the FRM II reactor in Garching (Germany). This paper presents the
principle of operation and a method for compensating the influence
of external magnetic fields on polarization using this device.

The system consists of three precession coils in a magnetic
screen. The first coil allows, by changing the current in it, to
ensure the rotation of the neutron spin by an arbitrary angle
relative to the magnetic field inside the coil. The remaining two
coils are designed to compensate for the effect of scattered
magnetic fields on the beam polarization, and to preserve the
polarization vector direction.
Vascularized pancreas-on-a-chip device produced using a printable simulated extracellular matrix
Authors: Hospodiuk-Karwowski Monika , Chi Kai , Pritchard Justin , Catchmark Jeffrey M
Published: August 2022

The extracellular matrix (ECM) influences cellular behavior, function, and fate. The ECM surrounding Langerhans islets has not been investigated in detail to explain its role in the development and maturation of pancreatic β-cells. Herein, a complex combination of the simulated ECM (sECM) has been examined with a comprehensive analysis of cell response and a variety of controls. The most promising results were obtained from group containing fibrin, collagen type I, Matrigel®, hyaluronic acid, methylcellulose, and two compounds of functionalized, ionically crosslinking bacterial cellulose (sECMbc). Even though the cell viability was not significantly impacted, the performance of group of sECMbc showed 2 to 4× higher sprouting number and length, 2 to 4× higher insulin secretion in static conditions, and 2 to 10× higher gene expression of VEGF-A, Endothelin-1, and NOS3 than the control group of fibrin matrix (sECMf). Each material was tested in a hydrogel-based, perfusable, pancreas-on-a-chip device and the best group—sECMbc has been tested with the drug Sunitinib to show the extended possibilities of the device for both diabetes-like screening as well as PDAC chemotherapeutics screening for potential personal medicine approach. It proved its functionality in seven days dynamic culture and is suitable as a physiological tissue model. Moreover, the device with the pancreatic-like spheroids was 3D bioprintable and perfusable.
Aptamer-functionalized quercetin thermosensitive liposomes for targeting drug delivery and antitumor therapy
Authors: Li Jian , Gao Yanting , Liu Shihe , Cai Jiahui , Zhang Qing , Li Kun , Liu Zhiwei , Shi Ming , Wang Jidong , Cui Hongxia
Published: August 2022

Chemo-thermotherapy, as a promising cancer combination therapy strategy, has attracted widespread attention. In this study, a novel aptamer functionalized thermosensitive liposome encapsulating hydrophobic drug quercetin was fabricated as an efficient drug delivery system. This aptamer-functionalized quercetin thermosensitive liposomes (AQTSL) combined the merits of high-loading yield, sustained drug release, long-term circulation in the body of PEGylated liposomes, passive targeting provided by 100–200 nm nanoparticles, active targeting and improved internalization effects offered by AS1411 aptamer, and temperature-responsive of quercetin release. In addition, AQTSL tail vein injection combined with 42 °C water bath heating on tumor site (AQTSL + 42 °C)treatment inhibited the tumor growth significantly compared with the normal saline administration (p < 0.01), and the inhibition rate reached 75%. Furthermore, AQTSL + 42 °C treatment also slowed down the tumor growth significantly compared with QTSL combined with 42 °C administration (p < 0.05), confirming that AS1411 decoration on QTSL increased the active targeting and internalization effects of the drug delivery system, and AS1411 aptamer itself might also contribute to the tumor inhibition. These data indicate that AQTSL is a potential carrier candidate for different hydrophobic drugs and tumor targeting delivery, and this kind of targeted drug delivery system combined with temperature responsive drug release mode is expected to achieve an ideal tumor therapy effect.
Untangling the impacts of socioeconomic and climatic changes on vegetation greenness and productivity in Kazakhstan
Authors: Venkatesh Kolluru , John Ranjeet , Chen Jiquan , Jarchow Meghann , Amirkhiz Reza Goljani , Giannico Vincenzo , Saraf Sakshi , Jain Khushboo , Kussainova Maira , Yuan Jing
Published: August 2022

Studies examining the joint interactions and impacts of social-environmental system (SES) drivers on vegetation dynamics in Central Asia are scarce. We investigated seasonal trends and anomalies in drivers and their impacts on ecosystem structure and function (ESF). We explored the response of net primary production, evapotranspiration and normalized difference vegetation index (NDVI) to various SES drivers—climate, human influence, heat stress, water storage, and water content—and their latent relationships in Kazakhstan. We employed 13 predictor drivers from 2000 to 2016 to identify the interactions and impacts on ESF variables that reflect vegetation growth and productivity. We developed 12 models with different predictor–response variable combinations and separated them into two approaches. First, we considered the winter percent snow cover (SNOWc) and spring rainfall (P_MAM) as drivers and then as moderators in a structural equation model (SEM). SNOWc variability (SNOWcSD) as an SEM moderator exhibited superior model accuracy and explained the interactions between various predictor–response combinations. Winter SNOWcSD did not have a strong direct positive influence on summer vegetation growth and productivity; however, it was an important moderator between human influence and the ESF variables. Spring rainfall had a stronger impact on ESF variability than summer rainfall. We also found strong positive feedback between soil moisture (SM) and NDVI, as well as a strong positive influence of vegetation optical depth (VOD) and terrestrial water storage (TWS) on ESF. Livestock density (LSKD) exhibited a strong negative influence on ESF. Our results also showed a strong positive influence of socioeconomic drivers, including crop yield per hectare (CROPh), gross domestic product per capita (GDPca), and population density (POPD) on vegetation productivity. Finally, we found that vegetation dynamics were more sensitive to SM, VOD, LSKD and POPD than climatic drivers, suggesting that water content and human influence drivers were more critical in Kazakhstan.
Postmitotic centriole disengagement and maturation leads to centrosome amplification in polyploid trophoblast giant cells
Authors: Buss Garrison , Stratton Miranda B. , Milenkovic Ljiljana , Stearns Tim
Published: August 2022

Trophoblast giant cells (TGCs) undergo endocycles resulting in polyploidy but their centriole state is unknown. We find that centrioles in endocycling TGCs undergo atypical interphase disengagement and conversion to single-centriole centrosomes. This gives an increased centrosome number but not tight coupling to DNA endocycling.
Gender History, Global History, and Atlantic Slavery
Authors: Paton Diana
Published: August 2022

Bringing into connection the scholarship on social reproduction and racial capitalism shows that the global history of Atlantic slavery is a gendered story; and the gendered history of Atlantic slavery is a global story. Attending in particular to reproductive labor in all its forms, and to the centrality of gender relations to the transmission of property and status, enables greater understanding of Atlantic slavery as a critically important aspect of modern global history. Indeed, without attention to gender and specifically to reproductive work, the global history of Atlantic slavery will inevitably be partial and incomplete. The reproductive work of women in Africa, as well as in the Americas, should be understood as an integral part of the development of Atlantic slavery, and thus of racial capitalism.
As If I Wasn’t There
Authors: Hodes Martha
Published: August 2022

Reflecting on the dilemmas faced by a historian writing a deeply researched memoir of a childhood event, this essay grapples with the difficulties of writing from childhood memory and addresses the ambivalence surrounding writing about oneself. Confronting the imperative to write about emotion—of both the child in the past and the historian in the present—the essay looks to the work of other scholars and writers for creative and effective models that combine history and memoir.
The Utility of SOX10 Immunohistochemical Staining in Breast Pathology
Authors: Rammal Rayan , Goel Kanika , Elishaev Esther , Rinda Soong T , Jones Mirka W , Zhao Chengquan , Clark Beth Z , Carter Gloria J , Yu Jing , Fine Jeffrey L , Villatoro Tatiana M , Harinath Lakshmi , Bhargava Rohit
Published: August 2022

Objectives

SOX10 expression helps identify melanocytic lesions. Over time, novel uses have been identified, such as expression in triple-negative breast cancer (TNBC). We evaluated the usefulness of SOX10 in breast pathology—specifically, identification and subtyping of TNBC and distinction from gynecologic carcinomas, use as a myoepithelial marker, and in the distinction of usual ductal hyperplasia (UDH) from atypical ductal hyperplasia (ADH).

Methods

Several breast and gynecologic carcinoma tissue microarrays containing a total of 492 cases were stained with SOX10. Whole sections of 34 ADH, 50 UDH, and 29 ductal carcinoma in situ (DCIS) samples were also stained with SOX10.

Results

SOX10 expression was identified in 67% of consecutive TNBC cases. Expression was mostly seen in nonapocrine, androgen receptor (AR)–negative TNBCs. All gynecologic carcinomas (n = 157) were negative. All UDH cases showed mosaic SOX10 expression, while all ADH cases lacked expression. All estrogen receptor (ER)–positive DCIS (n = 19) specimens were negative for SOX10, while 2 of 10 ER-negative DCIS specimens were positive for SOX10. The latter 2 cases showed SOX10-positive invasive carcinomas.

Conclusions

SOX10 identifies nonluminal AR-type TNBC and is useful in distinguishing TNBC from gynecologic carcinomas. SOX10 can distinguish UDH from ADH. SOX10 is not useful in distinguishing ADH from DCIS.
Investigating the Use of Grammar Learning Strategies in Hungary and Poland: A Comparative Study
Authors: Pawlak Mirosław , Csizér Kata
Published: August 2022

Although there is consensus that second language grammar instruction is needed, some controversial issues remain. Whatever instructional options are selected, it is vital that they allow the development of not only explicit knowledge but also implicit or at least automatized knowledge that can be used in real-time interaction. Since this aim is difficult to achieve, students need to learn this subsystem on their own and this process can be aided by adept use of grammar learning strategies (GLS). However, research in this area is scarce, existing tools have not been validated in different contexts, and no cross-country comparisons have been made. The study addresses these gaps by examining the use of GLS by university students majoring in English in Hungary (N = 205) and Poland (N = 173). Data were collected by means of a standardized questionnaire and subjected to principal component analysis and correlational analysis. Independent- and paired-samples t-tests as well as regression analyses were also run. Some differences were found between the two contexts but overall patterns of GLS use were strikingly similar.
Chemical footprints mediate habitat selection in co-occurring aphids
Authors: Porras Mitzy F , McCartney Nathaniel , Raspotnig Günther , Rajotte Edwin G
Published: August 2022

Habitat selection is a critical process that shapes the spatial distribution of species at local and regional scales. The mechanisms underlying habitat preference rely on environmental factors, species traits, and ecological interactions with other species. Here, we examined spatial segregation between two co-occurring aphid species (Rhopalosiphum maidis and R. padi) on wheat plants. We hypothesized that spatial segregation between these aphid species was mediated by aphid cuticular compounds left as chemical “footprints” on plant surfaces. Combining field and laboratory experiments, we first examined how plant microsites alter fitness by measuring the fecundity of each species. Next, we tested whether intra- and interspecific pre-inhabitation modified habitat selection in both aphid species. Both aphid species preferred and exhibited higher fecundity on wheat stems versus leaves. Laboratory trials showed that R. maidis pre-inhabitation altered R. padi spatial preference. By gas chromatography-mass spectrometry analysis and bioassays testing the effects of aphid density and footprint extracts, we found a density-dependent response, with R. padi avoiding locations previously inhabited by R. maidis. The chemical analysis of footprint crude extracts revealed a highly abundant compound, 1-hexacosanol, and when presented in the synthetic form, also elicited R. padi displacement. Altogether, it indicated that R. maidis footprints altered R. padi habitat selection with cuticular compounds playing a relevant role in the habitat selection process in co-occurring aphid species.
Anthropogenic noise and light alter temporal but not spatial breeding behavior in a wild frog
Authors: Cronin Andrew D , Smit Judith A H , Halfwerk Wouter
Published: August 2022

Increasing urbanization has led to large-scale land-use changes, exposing persistent populations to drastically altered environments. Sensory pollutants, including low-frequency anthropogenic noise and artificial light at night (ALAN), are typically associated with urban environments and known to impact animal populations in a variety of ways. Both ALAN and anthropogenic noise can alter behavioral and physiological processes important for survival and reproduction, including communication and circadian rhythms. Although noise and light pollution typically co-occur in urbanized areas, few studies have addressed their combined impact on species’ behavior. Here, we assessed how anthropogenic noise and ALAN can influence spatial and temporal variation in breeding activity of a wild frog population. By exposing artificial breeding sites inside a tropical rainforest to multiple sensory environments, we found that both anthropogenic noise and ALAN impact breeding behavior of túngara frogs (Engystomops pustulosus), albeit in different ways. Males arrived later in the night at their breeding sites in response to anthropogenic noise. ALAN, on the other hand, led to an increase in calling effort. We found no evidence that noise or light pollution either attracted frogs to or repelled frogs from breeding sites. Thus, anthropogenic noise may negatively affect calling males by shifting the timing of sexual signaling. Conversely, ALAN may increase the attractiveness of calling males. These changes in breeding behavior highlight the complex ways that urban multisensory pollution can influence behavior and suggest that such changes may have important ecological implications for the wildlife that are becoming increasingly exposed to urban multisensory pollution.
CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins
Authors: Zhang Tianjiao , Jia Yuran , Li Hongfei , Xu Dali , Zhou Jie , Wang Guohua
Published: August 2022

CRISPR-Cas system is an adaptive immune system widely found in most bacteria and archaea to defend against exogenous gene invasion. One of the most critical steps in the study of exploring and classifying novel CRISPR-Cas systems and their functional diversity is the identification of Cas proteins in CRISPR-Cas systems. The discovery of novel Cas proteins has also laid the foundation for technologies such as CRISPR-Cas-based gene editing and gene therapy. Currently, accurate and efficient screening of Cas proteins from metagenomic sequences and proteomic sequences remains a challenge. For Cas proteins with low sequence conservation, existing tools for Cas protein identification based on homology cannot guarantee identification accuracy and efficiency. In this paper, we have developed a novel stacking-based ensemble learning framework for Cas protein identification, called CRISPRCasStack. In particular, we applied the SHAP (SHapley Additive exPlanations) method to analyze the features used in CRISPRCasStack. Sufficient experimental validation and independent testing have demonstrated that CRISPRCasStack can address the accuracy deficiencies and inefficiencies of the existing state-of-the-art tools. We also provide a toolkit to accurately identify and analyze potential Cas proteins, Cas operons, CRISPR arrays and CRISPR-Cas locus in prokaryotic sequences. The CRISPRCasStack toolkit is available at https://github.com/yrjia1015/CRISPRCasStack.
ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery
Authors: Yan Huihui , Xie Yuanyuan , Liu Yao , Yuan Leer , Sheng Rong
Published: August 2022

An unsolved challenge in developing molecular representation is determining an optimal method to characterize the molecular structure. Comprehension of intramolecular interactions is paramount toward achieving this goal. In this study, ComABAN, a new graph-attention-based approach, is proposed to improve the accuracy of molecular representation by simultaneously considering atom–atom, bond–bond and atom-bond interactions. In addition, we benchmark models extensively on 8 public and 680 proprietary industrial datasets spanning a wide variety of chemical end points. The results show that ComABAN has higher prediction accuracy compared with the classical machine learning method and the deep learning-based methods. Furthermore, the trained neural network was used to predict a library of 1.5 million molecules and picked out compounds with a classification result of grade I. Subsequently, these predicted molecules were scored and ranked using cascade docking, molecular dynamics simulations to generate five potential candidates. All five molecules showed high similarity to nanomolar bioactive inhibitors suppressing the expression of HIF-1α, and we synthesized three compounds (Y-1, Y-3, Y-4) and tested their inhibitory ability in vitro. Our results indicate that ComABAN is an effective tool for accelerating drug discovery.
Small compound-based direct cell conversion with combinatorial optimization of pathway regulations
Authors: Nakamura Toru , Iwata Michio , Hamano Momoko , Eguchi Ryohei , Takeshita Jun-ichi , Yamanishi Yoshihiro
Published: August 2022

Motivation

Direct cell conversion, direct reprogramming (DR), is an innovative technology that directly converts source cells to target cells without bypassing induced pluripotent stem cells. The use of small compounds (e.g. drugs) for DR can help avoid carcinogenic risk induced by gene transfection; however, experimentally identifying small compounds remains challenging because of combinatorial explosion.

Results

In this article, we present a new computational method, COMPRENDRE (combinatorial optimization of pathway regulations for direct reprograming), to elucidate the mechanism of small compound-based DR and predict new combinations of small compounds for DR. We estimated the potential target proteins of DR-inducing small compounds and identified a set of target pathways involving DR. We identified multiple DR-related pathways that have not previously been reported to induce neurons or cardiomyocytes from fibroblasts. To overcome the problem of combinatorial explosion, we developed a variant of a simulated annealing algorithm to identify the best set of compounds that can regulate DR-related pathways. Consequently, the proposed method enabled to predict new DR-inducing candidate combinations with fewer compounds and to successfully reproduce experimentally verified compounds inducing the direct conversion from fibroblasts to neurons or cardiomyocytes. The proposed method is expected to be useful for practical applications in regenerative medicine.

Availability and implementation

The code supporting the current study is available at the http://labo.bio.kyutech.ac.jp/~yamani/comprendre.

Supplementary information

Supplementary data are available at Bioinformatics online.
Sertoli cells require TDP-43 to support spermatogenesis
Authors: Zomer Helena D , Osuru Hari Prasad , Chebolu Apoorv , Rayl Jeremy M , Timken Madeline , Reddi Prabhakara P
Published: August 2022

TAR DNA binding protein of 43 kD (TDP-43) is an evolutionarily conserved, ubiquitously expressed transcription factor and RNA-binding protein with major human health relevance. TDP-43 is present in Sertoli and germ cells of the testis and is aberrantly expressed in the sperm of infertile men. Sertoli cells play a key role in spermatogenesis by offering physical and nutritional support to male germ cells. The current study investigated the requirement of TDP-43 in Sertoli cells. Conditional knockout (cKO) of TDP-43 in mouse Sertoli cells caused failure of spermatogenesis and male subfertility. The cKO mice showed decreased testis weight, and low sperm count. Testis showed loss of germ cell layers, presence of vacuoles, and sloughing of round spermatids, suggesting loss of contact with Sertoli cells. Using a biotin tracer, we found that the blood-testis barrier (BTB) was disrupted as early as postnatal day 24 and worsened in adult cKO mice. We noted aberrant expression of the junction proteins connexin-43 (gap junction) and N-cadherin (ectoplasmic specialization). Oil Red O staining showed a decrease in lipid droplets (phagocytic function) in tubule cross-sections, Sertoli cells cytoplasm, and in the lumen of seminiferous tubules of cKO mice. Finally, qRT-PCR showed upregulation of genes involved in the formation and/or maintenance of Sertoli cell junctions as well as in the phagocytic pathway. Sertoli cells require TDP-43 for germ cell attachment, formation and maintenance of BTB, and phagocytic function, thus indicating an essential role for TDP-43 in the maintenance of spermatogenesis.
Was Henry David Thoreau a Good Naturalist? An Approach for Assessing Data from Historical Natural History Records
Authors: Primack Richard B , Miller-Rushing Abraham J , Miller Tara K
Published: August 2022

abstract

Ecologists are increasingly combining historical observations made by naturalists with modern observations to detect the ecological effects of climate change. This use of historical observations raises the following question: How do we know that historical data are appropriate to use to answer current ecological questions? In the present article, we address this question for environmental philosopher Henry David Thoreau, author of Walden. Should we trust his observations? We qualitatively and quantitatively evaluate Thoreau's observations using a three-step framework: We assess the rigor, accuracy, and utility of his observations to investigate changes in plants and animals over time. We conclude that Thoreau was an accurate observer of nature and a reliable scientist. More importantly, we describe how this simple three-step approach could be used to assess the accuracy of other scientists and naturalists.
When Law-And-Order Politics Fail: Media Fragmentation and Protective Factors That Limit the Politics of Fear
Authors: Lee Murray , Ellis Justin R , Keel Chloe , Wickes Rebecca , Jackson Jonathan
Published: August 2022

Law-and-order politics has long been a topic of scholarly work. The leveraging of fear of crime for political capital has been of particular concern. In the 2018 election in the Australian state of Victoria, crime and law-and-order became prominent political issues, particularly through racialized discourse about ‘African gangs’. That election provides a case study here. This article turns the traditional analysis of the politics of fear of crime around and considers some of the key reasons why law-and-order politics failed to gain decisive political traction in this instance. Media fragmentation and diversification continues to challenge the primacy of political primary definers in unpredictable ways. As such, electoral strategies that seek to leverage fear of crime and community insecurity need to be understood in the context of broader individual, community and social protective factors that might mitigate fear of crime.
Asteraceae as a model system for evolutionary studies: from fossils to genomes
Authors: Palazzesi Luis , Pellicer Jaume , Barreda Viviana D , Loeuille Benoît , Mandel Jennifer R , Pokorny Lisa , Siniscalchi Carolina M , Tellería M Cristina , Leitch Ilia J , Hidalgo Oriane
Published: August 2022

With c. 24 700 species (10% of all flowering plants), Asteraceae are one of the largest and most phenotypically diverse angiosperm families, with considerable economic and ecological importance. Asteraceae are distributed worldwide, from nearly polar latitudes all the way to the tropics, and occur across a diverse range of habitats from extreme deserts to swamps and from lowland rainforests to alpine tundra. Altogether, these characteristics make this family an outstanding model system to address a broad range of eco-evolutionary questions. In this review, we summarize recent progress in our understanding of Asteraceae on the basis of joint efforts by specialists in the fields of palaeobotany, cytogenetics, comparative genomics and phylogenomics. We will highlight how these developments are opening up new possibilities for integrating fields and better comprehending evolution beyond Asteraceae.
Preoperative brain connectome predicts postoperative changes in processing speed in moyamoya disease
Authors: Gao Mengxia , Lam Charlene L M , Lui Wai M , Lau Kui Kai , Lee Tatia M C
Published: August 2022

Moyamoya disease is a rare cerebrovascular disorder associated with cognitive dysfunction. It is usually treated by surgical revascularization, but research on the neurocognitive outcomes of revascularization surgery is controversial. Given that neurocognitive impairment could affect the daily activities of patients with moyamoya disease, early detection of postoperative neurocognitive outcomes has the potential to improve patient management. In this study, we applied a well-established connectome-based predictive modelling approach to develop machine learning models that used preoperative resting-state functional connectivity to predict postoperative changes in processing speed in patients with moyamoya disease. Twelve adult patients with moyamoya disease (age range: 23–49 years; female/male: 9/3) were recruited prior to surgery and underwent follow-up at 1 and 6 months after surgery. Twenty healthy controls (age range: 24–54 years; female/male: 14/6) were recruited and completed the behavioural test at baseline, 1-month follow-up and 6-month follow-up. Behavioural results indicated that the behavioural changes in processing speed at 1 and 6 months after surgery compared with baseline were not significant. Importantly, we showed that preoperative resting-state functional connectivity significantly predicted postoperative changes in processing speed at 1 month after surgery (negative network: ρ = 0.63, Pcorr = 0.017) and 6 months after surgery (positive network: ρ = 0.62, Pcorr = 0.010; negative network: ρ = 0.55, Pcorr = 0.010). We also identified cerebro-cerebellar and cortico-subcortical connectivities that were consistently associated with processing speed. The brain regions identified from our predictive models are not only consistent with previous studies but also extend previous findings by revealing their potential roles in postoperative neurocognitive functions in patients with moyamoya disease. Taken together, our findings provide preliminary evidence that preoperative resting-state functional connectivity might predict the post-surgical longitudinal neurocognitive changes in patients with moyamoya disease. Given that processing speed is a crucial cognitive ability supporting higher neurocognitive functions, this study’s findings offer important insight into the clinical management of patients with moyamoya disease.
Control of hybrid DC/AC microgrid system employing fuel cell and solar photovoltaic sources using grey wolf optimization
Authors: Al-Antaki Ahmed M , Golubchik T V , Al-Furaiji Mushtaq A , Mohammed H J
Published: August 2022

The outcome of this study is to improve and enhance the power quality of the hybrid DC/AC microgrid (MG). The photovoltaic (PV) system and the proton exchange membrane fuel cell (PEMFC) are used as renewable energy sources to deliver the optimum active power to the utility grid. The MG system based on the PV system, PEMFC and voltage source inverter is modelled mathematically. Also, the maximum power point tracking (MPPT)-based grey wolf optimization (GWO) is used to increase the PV module efficiency and enhance performance. Also, to improve the PEMFC performance, a digital proportional-integral controller is used to control the PEMFC circuit. The proposed inverter is controlled using synchronous reference frame theory, called the direct-quadrature (dq) control method. Hence, the performance of the proposed MG system is tested using MATLAB® for various weather and loading conditions. From the simulation results, the proposed MG system can deliver and absorb an active power based on the PV and fuel cell characteristics. As a result, the hybrid DC/AC MG is enhanced in terms of stabilization of the DC-bus voltage. Also, the power quality of the MG is improved using GWO optimization based on MPPT. Finally, good results are achieved using GWO in terms of the total harmonic distortion of the output current of 2.3% and higher efficiency of 98.9%.
Breaking Down the Breakpoints: Rationale for the 2022 Clinical and Laboratory Standards Institute Revised Piperacillin-Tazobactam Breakpoints Against Enterobacterales
Authors: Tamma Pranita D , Harris Patrick N A , Mathers Amy J , Wenzler Eric , Humphries Romney M
Published: August 2022

Piperacillin-tazobactam (PTZ) is one of the most common antibiotics administered to hospitalized patients. Its broad activity against gram-negative, gram-positive, and anaerobic pathogens; efficacy in clinical trials across diverse infection types and patient populations; and generally favorable toxicity profile make it a particularly appealing antibiotic agent. PTZ susceptibility interpretive criteria (ie, breakpoints) for the Enterobacterales were initially established in 1992, as the drug was undergoing approval by the US Food and Drug Administration. In the ensuing 30 years, changes in the molecular epidemiology of the Enterobacterales and its impact on PTZ susceptibility testing, mounting pharmacokinetic/pharmacodynamic data generated from sophisticated techniques such as population pharmacokinetic modeling and Monte Carlo simulation, and disturbing safety signals in a large clinical trial prompted the Clinical Laboratory and Standards Institute (CLSI) to review available evidence to determine the need for revision of the PTZ breakpoints for Enterobacterales. After an extensive literature review and formal voting process, the susceptibility criteria were revised in the 2022 CLSI M100 document to the following: ≤8/4 µg/mL (susceptible), 16/4 µg/mL (susceptible dose-dependent), and ≥32/4 µg/mL (resistant). Herein, we provide a brief overview of the CLSI process of antibiotic breakpoint revisions and elaborate on the available data that ultimately led to the decision to revise the PTZ breakpoints.
Reflections on the post-Covid city
Authors: Glaeser Edward L
Published: August 2022

What will COVID-19 and the shift to remote work do to the cities of the world? The temporary disruptions have been enormous and remain enormous as of the late summer of 2022. Offices remain vacant in many large cities. Within the US, the pandemic sped up the longer-term movement of people and firms to the sunbelt. Looking forward, there seem to be two possible scenarios, depending on the pandemic events of the future. If COVID-19 is only the first of a wave of deadly global disease events, then the urban renaissance that began thirty years ago could end. If COVID-19 is a one-off pandemic, then the impact of disease and telecommuting on urban life will be more limited. The enduring demand of people to enjoy urban amenities, and the value of learning face-to-face should enable cities to survive this shock. The stark gap between these two scenarios highlights the importance of global investments in public health that can reduce the risk of future pandemics.
Practical Blockchain-Based Steganographic Communication Via Adversarial AI: A Case Study In Bitcoin
Authors: Wang Minxian , Zhang Zijian , He Jialing , Gao Feng , Li Meng , Xu Shubin , Zhu Liehuang
Published: August 2022

With the development of 5G, the wireless Internet of Things (IoT) has become possible; how to provide privacy protections for the communication of IoT devices in a more vulnerable wireless transmission environment is a huge challenge. Thus, steganography is introduced as a safe and effective technology. Blockchain systems have been widely used in the area of steganography. Several works attempted to embed covert data into transactions in public blockchain systems such as Bitcoin, Ethereum and Monero. However, most of them merely focus on putting covert data into certain fields in transactions based on cryptographic algorithms. In this paper, a Covert Transaction Recognition (CTR) model is proposed by the Text Convolutional Neural Networks and Back Propagation Neural Networks. When utilizing the covert data-embedded field for recognizing, our CTR model can attain 0.79 precision and 0.83 recall on average for seven covert transaction construction schemes. The precision and recall can increase by at most 43 and 47%, respectively, if other unembedded fields were additionally exploited for recognition. We further propose a Practical Covert Transaction Construction (PCTC) model. This model fixes the contents in the embedded fields of the constructed transactions, and generates the contents in other fields using Generative Adversarial Networks. Experimental results demonstrated that the precision and recall are greatly decreased when identifying the covert transactions generated by our PCTC model. The data underlying this article are available in ‘covert-transaction-model’, at https://github.com/1997mint/covert-transaction-model.
Mechanisms shared between cancer, heart failure, and targeted anti-cancer therapies
Authors: de Wit Sanne , Glen Claire , de Boer Rudolf A , Lang Ninian N
Published: August 2022

Heart failure (HF) and cancer are the leading causes of death worldwide and accumulating evidence demonstrates that HF and cancer affect one another in a bidirectional way. Patients with HF are at increased risk for developing cancer, and HF is associated with accelerated tumour growth. The presence of malignancy may induce systemic metabolic, inflammatory, and microbial alterations resulting in impaired cardiac function. In addition to pathophysiologic mechanisms that are shared between cancer and HF, overlaps also exist between pathways required for normal cardiac physiology and for tumour growth. Therefore, these overlaps may also explain the increased risk for cardiotoxicity and HF as a result of targeted anti-cancer therapies. This review provides an overview of mechanisms involved in the bidirectional connection between HF and cancer, specifically focusing upon current ‘hot-topics’ in these shared mechanisms. It subsequently describes targeted anti-cancer therapies with cardiotoxic potential as a result of overlap between their anti-cancer targets and pathways required for normal cardiac function.
Mitochondrial calcium and reactive oxygen species in cardiovascular disease
Authors: Murphy Elizabeth , Liu Julia C
Published: August 2022

Cardiomyocytes are one of the most mitochondria-rich cell types in the body, with ∼30–40% of the cell volume being composed of mitochondria. Mitochondria are well established as the primary site of adenosine triphosphate (ATP) generation in a beating cardiomyocyte, generating up to 90% of its ATP. Mitochondria have many functions in the cell, which could contribute to susceptibility to and development of cardiovascular disease (CVD). Mitochondria are key players in cell metabolism, ATP production, reactive oxygen species (ROS) production, and cell death. Mitochondrial calcium (Ca2+) plays a critical role in many of these pathways, and thus the dynamics of mitochondrial Ca2+ are important in regulating mitochondrial processes. Alterations in these varied and in many cases interrelated functions play an important role in CVD. This review will focus on the interrelationship of mitochondrial energetics, Ca2+, and ROS and their roles in CVD. Recent insights into the regulation and dysregulation of these pathways have led to some novel therapeutic approaches.