bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain evolution and novel downstream processing with integrated catalysis enable highly efficient coproduction of 1,3‐propanediol and organic acid esters from crude glycerol
Authors: Zhang Chijian , Sharma Shubhang , Ma Chengwei , Zeng An‐Ping
Published: March 2022

Bioconversion of natural microorganisms generally results in a mixture of various compounds. Downstream processing (DSP) which only targets a single product often lacks economic competitiveness due to incomplete use of raw material and high cost of waste treatment for by‐products. Here, we show with the efficient microbial conversion of crude glycerol by an artificially evolved strain and how a catalytic conversion strategy can improve the total products yield and process economy of the DSP. Specifically, Clostridium pasteurianum was first adapted to increased concentration of crude glycerol in a novel automatic laboratory evolution system. At m3 scale bioreactor the strain achieved a simultaneous production of 1,3‐propanediol (PDO), acetic and butyric acids at 81.21, 18.72, and 11.09 g/L within only 19 h, respectively, representing the most efficient fermentation of crude glycerol to targeted products. A heterogeneous catalytic step was developed and integrated into the DSP process to obtain high‐value methyl esters from acetic and butyric acids at high yields. The coproduction of the esters also greatly simplified the recovery of PDO. For example, a cosmetic grade PDO (96% PDO) was easily obtained by a simple single‐stage distillation process (with an overall yield more than 77%). This integrated approach provides an industrially attractive route for the simultaneous production of three appealing products from the crude glycerol fermentation broth, which greatly improve the process economy and ecology.
CRISPR‐Mediated Enzyme Fragment Complementation Assay for Quantification of the Stability of Splice Isoforms
Authors: Tang Zhichao , Hegde Shalakha , Zhao Junxing , Zhu Shoutian , Johnson Kristen A. , Lorson Christian L. , Wang Jingxin
Published: March 2022

Small‐molecule splicing modulators exemplified by an FDA‐approved drug, risdiplam, are a new pharmacological modality for regulating the expression and stability of splice isoforms. We report a CRISPR‐mediated enzyme fragment complementation (EFC) assay to quantify the splice isoform stability. The EFC assay harnessed a 42 amino acid split of a β‐galactosidase (designate α‐tag), which could be fused at the termini of the target genes using CRISPR/cas9. The α‐tagged splice isoform would be quantified by measuring the enzymatic activity upon complementation with the rest of β‐galactosidase. This EFC assay retained all the sequences of introns and exons of the target gene in the native genomic environment that recapitulates the cell biology of the diseases of interest. For a proof‐of‐concept, we developed a CRISPR‐mediated EFC assay targeting the exon 7 of the survival of motor neuron 2 (SMN2) gene. The EFC assay is compatible with 384‐well plates and robustly quantified the splicing modulation activity of small molecules. In this study, we also discovered that a coumarin derivative, compound 4, potently modulated SMN2 exon 7 splicing at as low as 1.1 nM.
The biological effects of geomagnetic field exhibit an important potential for cancer and vascular diseases
Authors: Chen Enlin , Chen Zhe , Chen Linxi , Hu Xiaoling
Published: March 2022

Xu et al. recently demonstrated that cryptochrome 4 (CRY4) protein, as a light‐dependent magnetic receptor, can sense geomagnetic fields to guide night‐migratory songbirds' navigation and evolution by the formation of composite radical pairs and electron transport. We aim to comment on CRY4 through radical pairs and electron transport for magnetic sensitive in night‐migratory songbirds' migration and evolution. Additionally, we find that the role of magnetic fields is deeply concerning to the scientific community and very enlightening for the diagnosis and treatment of cancer and vascular disease. We believe that this commentary makes a significant contribution to the literature because it elaborates on the importance of the geomagnetic field to night‐migratory songbirds and extends the diagnostic and therapeutic value to cancer and vascular disease.
Prosthetic valve endocarditis: Literally a growing concern following transcatheter aortic valve replacement
Authors: Goldsweig Andrew M. , Baron Suzanne J.
Published: March 2022

Key Points

Prosthetic valve endocarditis (PVE) following transcatheter aortic valve replacement (TAVR) in low surgical risk patients is uncommon, occurring in 11 of 396 patients (2.8%) in the study by Medranda et al., but associated with high morbidity (6 of 11 with embolic strokes [55%]) and mortality (2 of 11 [18%]).

As TAVR volumes increase, especially in low surgical risk patients, whose long‐term outcomes are generally excellent, PVE will become an increasingly important concern.

Future research is needed to identify optimal strategies for prevention, diagnosis, and treatment of PVE associated with TAVR.
Atypical presentation of adenosine deaminase 2 deficiency with bi‐allelic ADA2 mutation
Authors: Al‐shaikh Reem , Alnowaiser Dimah , Peer‐Zada Abdul Ali , Almutairi Awatif , Alghamdi Hamza
Published: March 2022

Herein, we report a case of VAIHS with atypical clinical presentation of perianal abscess, fistula fever, and bi‐cytopenia including pathogenic ADA2 mutation suggesting that ADA2 deficiency be considered as a differential diagnosis of enlarging cutaneous abscess with no evidence of wound healing in the setting of leukopenia and neutropenia.
Metalloimmunotherapy with Rhodium and Ruthenium Complexes: Targeting Tumor‐Associated Macrophages
Authors: Toupin Nicholas , Herroon Mackenzie K. , Thummel Randolph P. , Turro Claudia , Podgorski Izabela , Gibson Heather , Kodanko Jeremy J.
Published: March 2022

Tumor associated macrophages (TAMs) suppress the cancer immune response and are a key target for immunotherapy. The effects of ruthenium and rhodium complexes on TAMs have not been well characterized. To address this gap in the field, a panel of 22 dirhodium and ruthenium complexes were screened against three subtypes of macrophages, triple‐negative breast cancer and normal breast tissue cells. Experiments were carried out in 2D and biomimetic 3D co‐culture experiments with and without irradiation with blue light. Leads were identified with cell‐type‐specific toxicity toward macrophage subtypes, cancer cells, or both. Experiments with 3D spheroids revealed complexes that sensitized the tumor models to the chemotherapeutic doxorubicin. Cell surface exposure of calreticulin, a known facilitator of immunogenic cell death (ICD), was increased upon treatment, along with a concomitant reduction in the M2‐subtype classifier arginase. Our findings lay a strong foundation for the future development of ruthenium‐ and rhodium‐based chemotherapies targeting TAMs.
Electrochemically Driven Swinging of a Nitrobenzyl Pendant Arm in a Nickel Scorpionand Complex
Authors: Ciarrocchi Carlo , Fabbrizzi Luigi , Licchelli Maurizio , Taglietti Angelo
Published: March 2022

A radical anion −NO2.− is formed upon an electrochemically reversible one‐electron reduction of the square‐planar NiII complex of N‐nitrobenzylcyclam. The −NO2.− group goes to occupy an axial position of the metal ion, thus establishing a significant electronic interaction with the metal center. In particular, the ESR spectrum supports the occurrence of an electron transfer from −NO2.− to the metal, which therefore presents a significant NiI character. On re‐oxidation, the nitrobenzyl side chain detaches and the NiII complex is restored, providing an example of a fully reversible redox driven intramolecular motion.
Mechanistic Insights into the Photoisomerization of N,N′‐Disubstituted Indigos
Authors: Budzák Šimon , Jovaišaitė Justina , Huang Chung‐Yang , Baronas Paulius , Tulaitė Kamilė , Juršėnas Saulius , Jacquemin Denis , Hecht Stefan
Published: March 2022

N,N′‐disubstituted indigos are photoswitchable molecules that have recently caught the attention due to their addressability by red‐light. When alkyl and aryl groups are utilized as the N‐substituents, the thermal half‐lives of Z isomers can be tuned independently while maintaining the advantageous red‐shifted absorption spectra. To utilize these molecules in real‐world applications, it is of immense importance to understand how their molecular structures as well as the environment influence their switching properties. To this end, we probed their photoisomerization mechanism by carrying out photophysical and computational studies in solvents of different polarities. The fluorescence and transient absorption experiments suggest for more polar excited and transition states, which explains the bathochromic shifts of absorption spectra and shorter thermal half‐lives. On the other hand, the quantum chemical calculations reveal that in contrast to N‐carbonyl groups, N‐alkyl and N‐aryl substituents are not strongly conjugated with the indigo chromophore and can thus serve as a tool for tuning the thermal stability of Z isomers. Both approaches are combined to provide in‐depth understandings of how indigos undergo photoswitching as well as how they are influenced by N‐substituent and the chemical surroundings. These mechanistic insights will serve as guiding principles for designing molecules eyeing broader applications.
Polymerization kinetics of tubulin from mung seedlings modeled as a competition between nucleation and GTP‐hydrolysis rates
Authors: Jain Kunalika , Basu Jashaswi , Roy Megha , Yadav Jyoti , Patil Shivprasad , Athale Chaitanya A.
Published: March 2022

Microtubules (MTs) form physiologically important cytoskeletal structures that are assembled by tubulin polymerization in nucleation‐ and guanosine triphosphate (GTP)‐dependent manner. GTP hydrolysis competes with the addition of monomers, to determine the GTP‐cap size, and the onset of shrinkage, which alternates with growth. Multiple theoretical models of MT polymerization dynamics have been reconciled to the kinetics of animal brain tubulins, but more recently, rapid kinetics seen in Arabidopsis tubulin polymerization suggest the need to sample a wider diversity in tubulin polymerization kinetics and reconcile it to theory. Here, we isolated tubulin from seedlings of Vigna sp. (mung bean), compared polymerization kinetics to animal brain tubulin, and used a computational model to understand the differences. We find that activity‐isolated mung tubulin polymerizes in a nucleation‐dependent manner, based on turbidimetry, qualitatively similar to brain tubulin, but with a 10‐fold smaller critical concentration. GTP‐dependent polymerization kinetics also appear to be transient, indicative of high rates of GTP hydrolysis. Computational modeling of tubulin nucleation and vectorial GTP hydrolysis to examine the effects of high nucleation and GTP‐hydrolysis rates predicts a dominance of the latter in determining MT lengths and numbers. Microscopy of mung tubulin filaments stabilized by GMPCPP or taxol results in few and short MTs, compared to the many long MTs arising from goat tubulin, qualitatively matching the model predictions. We find GTP‐hydrolysis outcompetes nucleation rates in determining MT lengths and numbers.
Dealloying Synthesis of Silicon Nanotubes for High‐Performance Lithium Ion Batteries
Authors: Zhao Jinfu , Wei Wenxian , Xu Na , Wang Xiaotong , Chang Limin , Wang Li , Fang Luan , Le Zaiyuan , Nie Ping
Published: March 2022

Practical applications of silicon‐based anodes in lithium ion batteries have attracted unprecedented attentions due to the merits of extraordinary energy density, high safety and low cost. Nevertheless, the inevitable huge volume change upon lithiation and delithiation brings about silicon electrode integrity damage and fast capacity fading, hampering the large‐scale application. Herein, a novel one‐dimensional tubular silicon‐nitrogen doped carbon composite (Si@NC) with a core‐shell structure has been fabricated using silicon magnesium alloy and polydopamine as a template and precursor. The as‐obtained composite exhibits remarkable specific capacity and ultrafast redox kinetics, an outstanding cycling stability with fine capacity of 583.6 mAh g−1 at 0.5 A g−1 over 200 cycles is delivered. Moreover, a full cell matched with LiFePO4 cathode has demonstrated a reversible capacity of 148.8 mAh g−1 with high Coulombic efficiency as well as an excellent energy density of 396 Wh kg−1. The nanotube structure engineering and silicon confined in nitrogen doped carbon effectively alleviate the volume expansion and endow the composite with superior stability. The robust strategy developed here gives a new insight into designing silicon anodes for enhanced lithium storage properties.
Stand up for Electrostatics: The Disiloxane Case
Authors: Martín‐Fernández Carlos , Alkorta Ibon , Montero‐Campillo M. Merced , Elguero José
Published: March 2022

The basicity of the simplest silicone, disiloxane (H3Si−O−SiH3), is strongly affected by the Si−O−Si angle (α). We use high‐level ab initio MP2/aug′‐cc‐pVTZ calculations and the molecular electrostatic potential (MEP) to analyze the relationship between the increase in basicity and the reduction of α. Our results clearly point out that this increase can be explained through the MEP, as the interactions between oxygen from disiloxane and the acceptors are mostly electrostatic. Furthermore, the effect of α on the tetrel bond between disiloxane and several Lewis bases can again be rationalized using the MEP. Finally, we explore the cooperativity throughout α for ternary complexes where disiloxane simultaneously interacts with a Lewis acid and a Lewis base. Both non‐covalent interactions remain cooperative for all α values, although the largest cooperativity effects are not always those maximizing the binding energy in the binary complexes. Overall, the MEP remains a powerful predictor for noncovalent interactions.
The influence of training variables on lingual strength and swallowing in adults with and without dysphagia
Authors: Abe Takashi , Viana Ricardo B. , Wong Vickie , Bell Zachary W. , Spitz Robert W. , Yamada Yujiro , Thiebaud Robert S. , Loenneke Jeremy P.
Published: March 2022

Background

Swallowing disorders (dysphagia) occur in a large proportion of individuals over the age of 60. The improvement of tongue strength by resistance exercise is postulated to be directly related to lingual‐palatal pressure generation and bolus propulsion into the pharynx during swallowing. To the best of our knowledge, however, there is no evidence‐based discussion evaluating the strength training variables of the tongue for improving tongue strength maximally.

Methods

To solve this problem, we reviewed the relationships between different resistance training variables (i.e. training period, intensity, duration of muscle contraction, volume, and frequency) and the change in muscle strength in the lingual muscle.

Results

Our findings show that tongue strength training may improve anterior and posterior tongue strength in both healthy adults and patients with dysphagia. Anterior and posterior tongue strength gradually increased and did not reach a plateau after at least 8 weeks of training. Data for other variables were insufficient to draw clear conclusions. Available data suggest that a training intensity of 60–100% of maximum tongue strength, a contraction time of 2–3 s, a total number of 90–120 repetitions per day, and a training frequency of three times per week appears to result in an improvement in maximal isometric tongue elevation strength in adults with and without dysphagia.

Conclusions

Future studies are warranted to better determine if there are dose–response relationships in tongue strength training in healthy adults and patients with dysphagia.
Significance of fluid retention, body mass index, and weight loss in patients with advanced cancer
Authors: Amano Koji , Maeda Isseki , Ishiki Hiroto , Miura Tomofumi , Hatano Yutaka , Oya Kiyofumi , Sakashita Akihiro , Ito Satoko , Hiratsuka Yusuke , Morita Tatsuya , Mori Masanori
Published: March 2022

Background

Few studies have investigated the relationship between body mass index (BMI) and mortality or evaluated the prognostic validity of a grading system incorporating BMI and weight loss in Asian cancer patients. We conducted a study to investigate characteristics according to BMI and to confirm the prognostic validity of BMI and the grading system.

Methods

This study involved a secondary analysis of a prospective cohort study. Subjects were divided into six BMI groups and five grades according to the grading system. Characteristics were compared between the six groups. We conducted time‐to‐event analyses using the Kaplan–Meier method, log‐rank test, and univariate and multivariate Cox regression analyses.

Results

A total of 1094 patients were classified into six BMI groups: <17 (n = 244), 17–18.4 (n = 211), 18.5–19.9 (n = 192), 20–21.9 (n = 196), 22–24.9 (n = 161), and 25 ≤ (n = 90). Regarding oedema, the prevalence increased with BMI, being 70% the 25 ≤ group. The prevalence of pleural effusion and ascites were the highest in the 25 ≤ group. Median survival ranged between 18 and 22 days in the six groups. No significant differences were observed in survival rates among the six BMI groups (log rank P = 0.83). No significant differences were observed in survival rates among the five grades (log rank P = 0.25).

Conclusions

The prevalence of fluid retention is high in patients with advanced cancer. BMI and weight loss appear to lose their prognostic significance among them.
Denervation‐induced loss of skeletal muscle mass influences immune homeostasis and accelerates the disease progression of lupus nephritis
Authors: Liu Shuang , Kiyoi Takeshi , Takemasa Erika , Mogi Masaki
Published: March 2022

Background

Patients with systemic autoimmune disease are predisposed to developing sarcopenia associated with their underlying proinflammatory condition and a decrease in motility. How sarcopenic status affects disease progression remains unknown. The present study explored the influence of denervation‐induced sarcopenia on immune homeostasis and investigated related biological pathways that might be important for future disease management.

Methods

A denervation‐induced skeletal muscle loss model was established, and the function of the immune system was evaluated. Immune cell proportions and cytokine levels in peripheral blood and atrophied skeletal muscle were profiled. We examined store‐operated Ca2+ entry and mitochondrial function in immune cells. MRL/lpr mice were used to evaluate the influence of denervation‐induced sarcopenia on autoimmune progression in lupus nephritis.

Results

Compared with splenocyte fractions obtained from sham mice, proportions of CD4+ cells, CD8+ cells, CD19+CD20− cells, CD49b+NK46+ cells, CD4+IL‐4+ cells, and CD4+FoxP3+ cells were significantly decreased, whereas CD19+CD20+ cells, CD4+IFN‐γ+ cells, and CD4+IL17+ cells were markedly increased in sciatic nerve axotomy (SNA) mice. The serum cytokine profile indicated that SNA significantly increased the protein expressions of IL‐12p70 (P = 0.014), IL‐17A (P = 0.007), and IFN‐γ (P < 0.001). In SNA mice, there was an 18.74% decrease in peak Ca2+ influx (P < 0.001) and an 18.22% decrease in initial Ca2+ influx (P < 0.001) rates in peripheral T cells compared with sham mice. Mitochondrial respiration was significantly reduced in peripheral T cells from SNA mice compared with sham mice. SNA substantially promoted disease progression in lupus model mice demonstrated by the results of proteinuria monitoring, serum levels of blood urea nitrogen, and kidney histological scores.

Conclusions

The loss of skeletal muscle impaired mitochondrial respiration and activation in T cells and influenced the balance of T helper cell subsets. Therefore, denervation‐induced sarcopenia might promote the progression of autoimmune diseases, such as lupus nephritis, and enhance Th1/Th17 functions. These results suggest that physicians should be aware of the impact of the loss of skeletal muscle on the management of autoimmune disease and that a multidisciplinary approach is required to minimize the overall adverse impact of sarcopenia.
The utility of the ultrasonographic assessment of the lower leg muscles to evaluate sarcopenia and muscle quality in older adults
Authors: Isaka Masaaki , Sugimoto Ken , Fujimoto Taku , Yasunobe Yukiko , Xie Keyu , Onishi Yuri , Yoshida Shino , Takahashi Toshimasa , Kurinami Hitomi , Akasaka Hiroshi , Takeya Yasushi , Yamamoto Koichi , Rakugi Hiromi
Published: March 2022

Background

The assessment of muscle quality is expected to help predict the prognosis of sarcopenia and examine the response to intervention. Ultrasonography can be used to evaluate approaches for determining muscle quantity and quality. We focused on the lower leg muscles and examined the relationship between the ultrasonographic assessments and the components of sarcopenia and muscle quality by comparing them with those of the quadriceps muscle (QFM).

Methods

47 physically healthy older participants aged 78.3 ± 6.0 years (53% male) were enrolled in this cross‐sectional study. Muscle thickness (MT) and echo intensity (EI) of the lower leg muscles and QFM were assessed with ultrasonography. Muscle mass, grip strength, and gait speed, and lower leg muscle strength were measured. Muscle quality was calculated using a formula: leg muscle strength/leg muscle mass.

Results

The MTs and EIs of the tibialis anterior muscle (TA) and QFM were significantly associated with grip and leg strength. We observed a significant correlation in the MTs and EIs of the lower leg muscles and QFM. The EIs of the lower leg muscles and QFM showed significant negative correlations with muscle quality. In the multiple linear regression model, the EI of the TA and QFM was extracted as an independent factor of muscle quality (TA: β = −0.35, p = 0.0358; QFM: β = −0.30, p = 0.0327).

Conclusions

The ultrasonographic assessments of the lower leg muscles, especially the TA, were associated with sarcopenia components and muscle quality equal to or greater than those of the QFM.
Ultrasound imaging for measuring muscle and subcutaneous fat tissue thickness of the anterior thigh: a 2 year longitudinal study in middle age
Authors: Mechelli Filippo , Arendt‐Nielsen Lars , Stokes Maria , Agyapong‐Badu Sandra
Published: March 2022

Background

Ultrasound (US) imaging technique is widely used in research and clinical settings to assess the morphology and morphometry of neuromusculoskeletal structures. The technique has reported validity and reliability in measuring the size of various muscles under controlled conditions. The aim of the present study was to assess anterior thigh thickness using US imaging, in a healthy cohort of middle‐aged older adults.

Methods

Participants included 17 healthy older adults involved in regular moderate‐vigorous activities (age range 39–66 years). US imaging scans of the anterior thighs 2 years since baseline measurements were performed. Images were analysed offline to compare US imaging measurements of muscle thickness and subcutaneous fat (SF) of the anterior thigh taken at baseline and after 2 years.

Results

There was no significant difference between muscle thickness measurements taken at baseline and after 2 years (mean, standard deviation; baseline = 2.80 ± 0.71 cm; follow‐up = 2.77 ± 0.72 cm, P = 0.33). There was also no significant change in SF thickness (baseline = 1.04 ± 0.41 cm; follow‐up = 1.06 ± 0.40, P = 0.33).

Conclusions

The results show that there was no decline in anterior thigh muscle thickness or increase in SF in the healthy cohort studied using US imaging over a 2 year period. These findings demonstrate the robustness of US imaging measurements over time.
Responsive curriculum development for professional education: Different teams, different tales
Authors: Vreuls Joyce , Koeslag‐Kreunen Mieke , van der Klink Marcel , Nieuwenhuis Loek , Boshuizen Henny
Published: March 2022

Due to fast and unpredictable developments, professional education is challenged with being responsive, which demands a rethinking of conventional curriculum development approaches. Yet, literature on curriculum development falls short in terms of recognising how to react rapidly and adequately to these new developments. This study focuses on curriculum development initiatives at the school level in a Dutch university of applied sciences. Open interviews were held with 29 curriculum developers to explore how they define and give substance to developing curricula for new, changing or unpredictable professions. These 29 participants were involved in seven curriculum development trajectories. Four themes were detected: (1) curriculum developers are in favour of open, flexible and authentic curricula; (2) the context in which the curriculum development takes place and the different roles and responsibilities of curriculum developers are challenging; (3) curriculum developers feel insufficiently equipped to carry out their tasks; and (4) involving stakeholders is necessary but results in a “viscous” social–political process. Responsive curriculum development requires a great deal of flexibility and adaptability from curriculum developers. Yet, in our study, “institutional concrete” is found to severely hinder responsive curriculum development processes. To be responsive, such processes need to be supported and institutional barriers need to be removed.
Acute transient thyroid swelling after fine‐needle aspiration biopsy: A case report of a rare complication and a literature review
Authors: Zeng Wenli , Lu Jinming , Yan Ziyan , Liu Yanna , Deng Wenfeng , Zhou Yi , Xu Wenwei , Wang Yuchen , Xu Jian , Miao Yun
Published: March 2022

Fine‐needle aspiration biopsy (FNAB) is a safe and effective thyroid examination method with rare complications. Herein, we report a rare case of acute transient thyroid swelling that occurred after ultrasound‐guided FNAB. The patient experienced acute pain with rapid thyroid swelling. Ultrasound imaging revealed a nodule with a linear, hypoechoic, and “patch‐like” appearance, indicating edema without hemorrhage. After receiving anti‐anaphylaxis and detumescence therapy for 1 day, the swelling regressed. Acute transient thyroid swelling is an extremely rare event that occurs shortly after FNAB and may frighten patients; therefore, clinicians should be aware of this complication in this context.
Cicada nymphs dominate American black bear diet in a desert riparian area
Authors: Lundgren Erick J. , Moeller Karla T. , Clyne Michael Otis , Middleton Owen S. , Mahoney Sean M. , Kwapich Christina L.
Published: March 2022

American black bears are considered dependent on high‐elevation forests or other montane habitats in the drylands of western North America. Black bear sign, including that of cubs, was observed throughout the summers of 2015, 2016, and 2018 along a perennial desert river in the Sonoran Desert of Arizona. We analyzed the contents of 21 black bear scats, collected from May to October of 2016 and 2018. Apache cicada nymphs (Diceroprocta apache) were the dominant food item, occurring in 90% of scats and comprising an average of 59% of scat contents. In the process of excavating these nymphs, bears created large areas of turned‐over soil, a form of ecosystem engineering with potential implications for soils, vegetation, and fluvial geomorphology. Given that species distributions are shaped by physiological and ecological contexts, as well as anthropogenic legacies, it is possible that black bears once occurred more commonly in desert riparian systems prior to widespread agricultural development, hunting, and dewatering. Although more research is necessary, we suggest that desert riparian systems may be an alternative habitat for black bears. Better understanding the diet and habitat breadth of American black bears is important in the context of increasing landscape fragmentation and militarization in the U.S.‐Mexican borderlands.
Amplicon_sorter: A tool for reference‐free amplicon sorting based on sequence similarity and for building consensus sequences
Authors: Vierstraete Andy R. , Braeckman Bart P.
Published: March 2022

Oxford Nanopore Technologies (ONT) is a third‐generation sequencing technology that is gaining popularity in ecological research for its portable and low‐cost sequencing possibilities. Although the technology excels at long‐read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high‐quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference‐free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.
Seed dormancy varies widely among Arabidopsis thaliana populations both between and within Fennoscandia and Italy
Authors: Zacchello Giulia , Bomers Svenja , Böhme Cecilia , Postma Froukje M. , Ågren Jon
Published: March 2022

The timing of germination is a key life‐history trait in plants, which is strongly affected by the strength of seed dormancy. Continental‐wide genetic variation in seed dormancy has been related to differences in climate and the timing of conditions suitable for seedling establishment. However, for predictions of adaptive potential and consequences of climatic change, information is needed regarding the extent to which seed dormancy varies within climatic regions and the factors driving such variation.

We quantified dormancy of seeds produced by 17 Italian and 28 Fennoscandian populations of Arabidopsis thaliana when grown in the greenhouse and at two field sites in Italy and Sweden. To identify possible drivers of among‐population variation in seed dormancy, we examined the relationship between seed dormancy and climate at the site of population origin, and between seed dormancy and flowering time.

Seed dormancy was on average stronger in the Italian compared to the Fennoscandian populations, but also varied widely within both regions. Estimates of seed dormancy in the three maternal environments were positively correlated. Among Fennoscandian populations, seed dormancy tended to increase with increasing summer temperature and decreasing precipitation at the site of population origin. In the smaller sample of Italian populations, no significant association was detected between mean seed dormancy and climate at the site of origin. The correlation between population mean seed dormancy and flowering time was weak and not statistically significant within regions.

The correlation between seed dormancy and climatic factors in Fennoscandia suggests that at least some of the among‐population variation is adaptive and that climate change will affect selection on this trait. The weak correlation between population mean seed dormancy and flowering time indicates that the two traits can evolve independently.
Evaluation of a hydrogen signal detection method using a compact NMR sensor for the measurement of ion concentrations in culture medium
Authors: Ohkawara Seiichi , Miura Kentaro , Hirano Harutoyo , Ota Satoshi , Futagawa Masato
Published: March 2022

In recent years, the demand for highly nutritious and functional vegetables has been increasing in the agricultural sector. In order to cultivate highly functional vegetables, it is necessary to adjust the nutrients in the soil, such as potassium ions, to an optimal state. Therefore, there is a need for a sensor that can measure soil ion concentration in real time in the field. In this report, we aim to develop an ion concentration sensor using Nuclear Magnetic Resonance (NMR). Since the sensor observes atomic specific behavior, it has the potential to measure the concentration of each ion species in soil where multiple ions exist. In this study, we aim to realize compact NMR and to establish a method for NMR measurement of water ahead of ion measurement. Using an NMR measurement system of our own design, we measured water and air. As a result, NMR signal spectra were obtained only when measuring water under resonance conditions, and resonance frequency of hydrogen atoms were successfully measured. We have established an NMR signal measurement method for measuring ion concentrations using a small NMR sensor that can be installed in the agriculture.
Competition–colonization dynamics and multimodality in diversity–disturbance relationships
Authors: Liao Jinbao , Barabás György , Bearup Daniel
Published: March 2022

Disturbance has long been recognized as a critical driver of species diversity in community ecology. Recently, it has been found that the well‐known intermediate disturbance hypothesis, which predicts a unimodal diversity–disturbance relationship (DDR), fails to describe numerous experimental observations, as empirical DDRs are diverse. Consequently, the precise form of the DDR remains a topic of debate. Here we develop a simple yet comprehensive metacommunity framework that can account for complex competition patterns. Using both numerical simulations and analytical arguments, we show that strongly multimodal DDRs arise naturally, and this multimodality is quite robust to changing parameters or relaxing the assumption of a strict competitive hierarchy. Having multimodality as a robust property of DDRs in competition models suggests that much of the noise observed in empirical DDRs could be a critical signature of the underlying competitive dynamics.
Temporal changes of genetic structure and diversity in a marine diatom genus discovered via metabarcoding
Authors: Ruggiero Maria Valeria , Kooistra Wiebe H.C.F. , Piredda Roberta , Sarno Diana , Zampicinini Gianpaolo , Zingone Adriana , Montresor Marina
Published: March 2022

Diatoms’ bloom dynamics, with seasonal cycling of waxes and wanes of cell abundance, imply frequent bottleneck and expansion events that can leave signatures in the genetic structure and diversity of populations. We explored changes in genetic diversity and structure within multiple species of the planktonic marine diatom genus Pseudo‐nitzschia living in sympatry in the Gulf of Naples (Tyrrhenian Sea, Italy) over 48 sampling dates (from 2011 to 2013) by means of metabarcode data. The genus Pseudo‐nitzschia includes complexes of cryptic species along with morphologically distinguishable ones. We assessed the resolution power of the hypervariable V4 region of the 18S rDNA in delimiting species using different algorithms and a set of reference sequences. We measured intra‐specific genetic diversity and differentiation among species over three annual cycles. Between‐species divergence was higher in the P. pseudodelicatissima complex, while signs of incomplete lineage sorting and/or introgression were detected in the P. delicatissima complex. Most of the species showed significant population differentiation over time, due to changes in haplotypic composition over the three years. Some haplotypes were lost and new ones appeared, with high polymorphism in species of the P. delicatissima complex. We hypothesize that the observed temporal changes in genetic structure result from frequent founder events linked to a population dynamic characterized by cyclical alternation of clonal expansions and bottlenecks and discuss possible factors affecting the microevolutionary pathways in these planktonic diatoms.
A proposal of a new gradient driver with a gradational voltage inverter for low power loss
Authors: Oishi Masayuki , Kobayashi Ryosuke , Sakashita Tomokazu
Published: March 2022

This paper proposes a new gradient driver with a gradational voltage inverter for low power loss and downsized filter circuits. Gradient drivers produce direct current with low ripple amplitudes to achieve high image quality and high slew rates to obtain images rapidly. The proposed gradient driver is characterized by low ripple amplitude of the output current from the inverter composed of SiC‐MOSFETs and high output voltage from another inverter composed of IGBTs. This paper discusses both the principle of operation and control method of the new gradient driver. Experimental verification is performed on a full‐scale system. The results show the advantages of the proposed gradient driver based on loss analysis by calculations.
Construction of 3D Shape‐Changing Hydrogels via Light‐Modulated Internal Stress Fields
Authors: Xu Zihan , Fan Wenxin , Duan Jinghua , Xia Yanzhi , Nie Zhihong , Sui Kunyan
Published: March 2022

The 3D shape‐changing hydrogels are highly pursued for numerous applications. However, up to now, the construction of complex 3D shape‐changing hydrogels remains a challenge. The reported design strategies are mainly applied to fabricate 2D ones by introducing anisotropic microstructures into hydrogel sheets/membranes. Herein, we present a convenient photolithography strategy for constructing complex 3D shape‐changing hydrogels by simultaneously modulating anisotropic microstructures and internal stress fields of gel sheets. When the precursor solution containing ultraviolet (UV) absorber is irradiated by single‐side UV light, the attenuated polymerization rate can cause the generation of asymmetric internal stress field in the resulting hydrogel sheet. In the meantime, the directional diffusion of unpolymerized monomers allows for the formation of vertical gradient structure within hydrogel. Therefore, by applying different photomasks to modulate the local gradient structures and internal stress fields of the gel sheets, they can spontaneously transform into various complex 3D shape‐changing hydrogels in the air. Response to the external stimuli, these 3D shape‐changing hydrogels (e.g., fighter plane, birdie, and multi‐storey origami lattices) can deform in a novel 3D1‐to‐3D2‐to‐3D3 mode. This new design strategy contributes to the development of complex biomedical implants and soft robotics.
Development of a Quasi–Quantitative Structure–Activity Relationship Model for Prediction of the Immobilization Response of Daphnia magna Exposed to Metal-Based Nanomaterials
Authors: Bunmahotama Warisa , Vijver Martina G. , Peijnenburg Willie
Published: March 2022

The conventional Hill equation model is suitable to fit dose–response data obtained from performing (eco)toxicity assays. Models based on quasi–quantitative structure–activity relationships (QSARs) to estimate the Hill coefficient (nH) were developed with the aim of predicting the response of the invertebrate species Daphnia magna to exposure to metal-based nanomaterials. Descriptors representing the pristine properties of nanoparticles and media conditions were coded to a quasi–simplified molecular input line entry system and correlated to experimentally derived values of nH. Monte Carlo optimization was used to model the set of nH values, and the model was trained on the basis of reported dose–response relationships of 60 data sets (n = 367 individual response observations) of 11 metal-based nanomaterials as obtained from 20 literature reports. The model simulates the training data well, with only 2.3% deviation between experimental and modeled response data. The technique was employed to predict the dose–response relationships of 15 additional data sets (n = 72 individual observations) not included in model development of seven metal-based nanomaterials from 10 literature reports, with an average error of 3.5%. Combining the model output with either the median effective concentration value or any other known effect level as obtained from experimental data allows the prediction of full dose–response curves of D. magna immobilization. This model is an accurate screening tool that allows the determination of the shape and slope of dose–response curves, thereby greatly reducing experimental effort in case of novel advanced metal-based nanomaterials or the prediction of responses in altered exposure media. This screening model is compliant with the 3Rs (replacement, reduction, and refinement) principle, which is embraced by the scientific and regulatory communities dealing with nano-safety. Environ Toxicol Chem 2022;41:1439–1450. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Effects of physical exercise on muscle metabolism and meat quality characteristics of Mongolian sheep
Authors: Zhang Min , Guo Yueying , Su Rina , Corazzin Mirco , Li Jiale , Huang Huan , Zhang Yue , Yao Duo , Su Lin , Zhao Lihua , Jin Ye
Published: March 2022

The objective of this study was to investigate the effects of exercise training on muscle metabolism, fatty acid composition, carcass traits, and meat quality characteristics of Mongolian sheep. Fourteen Mongolian sheep were randomly divided into two groups (7 sheep in each) and placed in two adjacent livestock pens. One group of sheep was kept in the pen (Control [C] group) and the other group of sheep (Training [T] group) were driven away in a field to walk twice a day. The results showed a reduction in pH measured 45 min post mortem, L*, a*, and b* value, intramuscular fat, and carcass length, and an increase in the ultimate pH value and shear force in the meat of T group in comparison with that of C group (p < .050). Also, exercise training moderately affected the fatty acid composition of LT muscle. Compared with C group, the concentrations of myristoleic acid (C14:1) and stearic acid (C18:0) were increased (p < .050), while the concentrations of C20:3 n‐6, neurolic acid (C24:1), and n‐3 polyunsaturated fatty acid (PUFA) were decreased in T group (p < .050). Transcriptome analysis highlighted 621 genes differentially expressed in two groups, including 385 were up‐regulated (e.g., GLUT4 and PGC‐1α) and 236 were down‐regulated (e.g., PLIN1 and ACSL3) in T with respect to C group. Besides, considering these genes, a number of enrichment pathways related to muscle metabolic processes, involving carbohydrate metabolism, lipid metabolism, oxidation reduction process, and muscle tissue development, were highlighted. In conclusion, these results contributed to a better understanding of the possible biological and molecular processes underlying the effects of exercise training on muscle metabolism and meat quality in Mongolian sheep, and provide useful information for contributing to understand the phenotypic and functional differences in meat quality of sheep.
Evaluation of passion fruit mesocarp flour on the paste, dough, and quality characteristics of dried noodles
Authors: Ning Xin , Zhou Yahan , Wang Zhen , Zheng Xiaodong , Pan Xiaoli , Chen Zhilin , Liu Qiuping , Du Wei , Cao Xiaohuang , Wang Lei
Published: March 2022

Reasonable intake of high‐fiber staple food is already one of the most effective measures in fiber deficiency disease prevention and control. Passion fruit mesocarp flour (PFMF), the primary byproduct during passion fruit processing, was utilized to manufacture high‐fiber dried noodles. The presence of PFMF boosted wheat flour gelatinization and retrogradation. The competition for water between PFMF and wheat flour inhibited the formation of the gluten network, which harmed the cooking properties and decreased consumer acceptance of the resulting dried noodles. Nevertheless, PFMF fortification could considerably increase the dietary fiber content of noodles. Especially for noodles with 9% PFMF, the total dietary fiber content was greater than 6%, and they thus could be regarded as a high‐dietary‐fiber food. Generally, the current work demonstrates the feasibility of fabricating PFMF‐enriched dried noodles and their nutritional superiority compared to the corresponding normal product.
Identification of novel prostate cancer genes in patients stratified by Gleason classification: Role of antitumoral genes
Authors: Díaz de la Guardia‐Bolívar Elisa , Barrios‐Rodríguez Rocío , Zwir Igor , Jiménez‐Moleón José Juan , del Val Coral
Published: March 2022

Prostate cancer (PCa) is a tumor with a great heterogeneity, both at a molecular and clinical level. Despite its global good prognosis, cases can vary from indolent to lethal metastatic and scientific efforts are aimed to discern those with worse outcomes. Current prognostic markers, as Gleason score, fall short when it comes to distinguishing these cases. Identification of new early biomarkers to enable a better PCa distinction and classification remains a challenge. In order to identify new genes implicated in PCa progression we conducted several differential gene expression analyses over paired samples comparing primary PCa tissue against healthy prostatic tissue of PCa patients. The results obtained show that this approach is a serious alternative to overcome patient heterogeneity. We were able to identify 250 genes whose expression varies along with tissue differentiation—healthy to tumor tissue, 161 of these genes are described here for the first time to be related to PCa. The further manual curation of these genes allowed to annotate 39 genes with antitumoral activity, 22 of them described for the first time to be related to PCa proliferation and metastasis. These findings could be replicated in different cohorts for most genes. Results obtained considering paired differential expression, functional annotation and replication results point to: CGREF1, UNC5A, C16orf74, LGR6, IGSF1, QPRT and CA14 as possible new early markers in PCa. These genes may prevent the progression of the disease and their expression should be studied in patients with different outcomes.
Saturnenes Like Th@Au6D6h: Ring‐Current Evidence for Au−Au Bonding Along the Gold Ring
Authors: Pyykkö Pekka , Taubert Stefan
Published: March 2022

The electronic structure and stability of M′@Mn systems is considered using DFT. The metal atom M′ is a rare earth, actinide, or a d transition metal, and M is a coinage (Group 11) metal. The σ aromaticity along the Mn ring is emphasized. As a further indicator for it, the magnetically induced currents along the ring are studied, and found to be considerably larger than the aromatic π currents in benzene. A name saturnenes is suggested for these atom‐inside‐ring systems. Attention is also called for the known analogous stick‐inside‐ring systems.
Predicting microbiome compositions from species assemblages through deep learning
Authors: Michel‐Mata Sebastian , Wang Xu‐Wen , Liu Yang‐Yu , Angulo Marco Tulio
Published: March 2022

Microbes can form complex communities that perform critical functions in maintaining the integrity of their environment or their hosts' wellbeing. Rationally managing these microbial communities requires improving our ability to predict how different species assemblages affect the final species composition of the community. However, making such a prediction remains challenging because of our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. To overcome this challenge, we present a deep learning framework that automatically learns the map between species assemblages and community compositions from training data only, without knowing any of the above processes. First, we systematically validate our framework using synthetic data generated by classical population dynamics models. Then, we apply our framework to data from in vitro and in vivo microbial communities, including ocean and soil microbiota, Drosophila melanogaster gut microbiota, and human gut and oral microbiota. We find that our framework learns to perform accurate out‐of‐sample predictions of complex community compositions from a small number of training samples. Our results demonstrate how deep learning can enable us to understand better and potentially manage complex microbial communities.