bluuebunny/crossref_metadata_2025 huggingface dataset:
Active meta-learning for predicting and selecting perovskite crystallization experiments
Authors: Shekar Venkateswaran , Nicholas Gareth , Najeeb Mansoor Ani , Zeile Margaret , Yu Vincent , Wang Xiaorong , Slack Dylan , Li Zhi , Nega Philip W. , Chan Emory M. , Norquist Alexander J. , Schrier Joshua , Friedler Sorelle A.
Published: January 2022

Autonomous experimentation systems use algorithms and data from prior experiments to select and perform new experiments in order to meet a specified objective. In most experimental chemistry situations, there is a limited set of prior historical data available, and acquiring new data may be expensive and time consuming, which places constraints on machine learning methods. Active learning methods prioritize new experiment selection by using machine learning model uncertainty and predicted outcomes. Meta-learning methods attempt to construct models that can learn quickly with a limited set of data for a new task. In this paper, we applied the model-agnostic meta-learning (MAML) model and the Probabilistic LATent model for Incorporating Priors and Uncertainty in few-Shot learning (PLATIPUS) approach, which extends MAML to active learning, to the problem of halide perovskite growth by inverse temperature crystallization. Using a dataset of 1870 reactions conducted using 19 different organoammonium lead iodide systems, we determined the optimal strategies for incorporating historical data into active and meta-learning models to predict reaction compositions that result in crystals. We then evaluated the best three algorithms (PLATIPUS and active-learning k-nearest neighbor and decision tree algorithms) with four new chemical systems in experimental laboratory tests. With a fixed budget of 20 experiments, PLATIPUS makes superior predictions of reaction outcomes compared to other active-learning algorithms and a random baseline.
Electrochemical proton insertion modulates the hydrogen evolution reaction on tungsten oxides
Authors: Spencer Michael A. , Fortunato Jenelle , Augustyn Veronica
Published: January 2022

The development of new electrocatalysts for the hydrogen evolution reaction (HER) could reduce the dependence on Pt and other rare metals and enable large-scale production of hydrogen with near-zero carbon emissions. Mechanistic insight into the electrocatalytic activity of a material helps to accelerate the development of new electrocatalysts. Alternative electrocatalyst materials such as transition metal oxides and sulfides can undergo insertion reactions that change their properties. Recent reports indicate that the presence of inserted ions can influence the electrocatalytic activity. Here, we utilized a materials chemistry approach to understand the role of proton insertion in the HER activity of the layered tungsten oxide hydrates (WO3·xH2O, x = 1, 2). We synthesized a series of tungsten oxide hydrates along with an octylamine-pillared tungsten oxide (OA–WO3). We used cyclic voltammetry to study the electrochemical reactivity of each material and performed ex situ x-ray diffraction and Raman spectroscopy to understand bulk and surface structural changes during electrochemical cycling. We show an inverse relationship between the degree of proton insertion and HER overpotential in tungsten oxides: the lack of proton insertion leads to a high overpotential for the HER. We discuss three hypotheses for how proton insertion leads to the HER activity in WO3·xH2O: (1) proton insertion changes the electronic band structure of WO3·xH2O, (2) the presence of bulk protons can influence ΔGH,ads at the surface sites, and (3) the inserted protons may participate in the HER mechanism on WO3·xH2O. Overall, this work shows the critical role of proton insertion in enabling the high HER activity in tungsten oxides.
Validation of the Swedish Watson Dysphagia Scale for adult patients with eosinophilic esophagitis
Authors: Albinsson Sofie , Tuomi Lisa , Wennerås Christine , Larsson Helen
Published: January 2022

Background: The Swedish Watson Dysphagia Scale (S-WDS) has been used to assess dysphagia in patients with eosinophilic esophagitis (EoE) but has not been validated for this patient group. The aim of this study was to validate the S-WDS for adult patients with EoE. Methods: Ninety-seven Swedish adult patients with EoE and 97 controls without dysphagia filled out the S-WDS, the Swedish Eosinophilic Esophagitis Activity Index (S-EEsAI) and a set of supplementary questions. The reliability of the S-WDS was evaluated using Cronbach’s alpha, Pearson correlation of items and total score, and test–retest analysis (n = 29). Validity was investigated using Spearman correlations of the S-WDS items, S-EEsAI domains and a self-assessment score, and by investigating floor and ceiling effects. Results: The Cronbach’s alpha of the S-WDS was 0.77 and all items demonstrated moderate to strong correlation to the S-WDS score (r = 0.40–0.81) indicative of sufficient reliability of the instrument. In addition, the test–retest results reflected excellent reliability with an intraclass correlation coefficient of 0.85 for the S-WDS score. Adequate validity of the instrument was demonstrated, the S-WDS score correlated moderately with the self-assessment score and with 4/6 S-EEsAI domains, and strongly with the remaining two domains. Floor effects were more common for liquids and soft-textured foods and ceiling effects increased with increasing food consistency. The S-WDS scores of the patient group were significantly different from those of the nondysphagia control group (P < 0.001). Conclusion: The S-WDS instrument is an appropriate and valid instrument for assessment of dysphagia in patients with EoE.
Hiatal hernias associated with acid reflux: size larger than 2 cm matters
Authors: Shahsavari Dariush , Smith Michael S , Malik Zubair , Parkman Henry P
Published: January 2022

Hiatal hernia (HH) is associated with gastroesophageal reflux disease (GERD); the effect of HH size on GERD is not well defined. To evaluate the relationship between HH size as measured by high-resolution esophageal manometry (HREM) and reflux parameters on esophageal pH-impedance testing (multichannel intraluminal impedance-pH [MII-pH]) to define HH sizes associated with GERD. HREM and MII-pH studies were reviewed. The relationship of HH size to other parameters was analyzed with multivariable logistic regression. Correlation coefficients were determined using Spearman and Pearson’s tests. A total of 897 patients underwent both HREM and MII-pH. There were 529 (58.9%) patients with HH size <1 cm, 203 (22.6%) with HH 1.0–1.9 cm, and 165 (18.4%) with HH ≥2 cm. Larger HH size was associated with lower esophageal sphincter (LES) basal and residual pressures (r = −0.43 and r = −0.48, p < 0.01), higher acid exposure time (AET) (r = 0.17, p < 0.01), number of acidic refluxes (r = 0.16, p < 0.05), and number of reflux episodes detected by impedance (total r = 0.22, p < 0.01). HH ≥ 2 cm compared with smaller size HH was associated with higher proximal AET%, acidic refluxes, and reflux episodes detected by impedance (p < 0.05). Increasing HH size was associated with older age, higher AET, and number of reflux episodes. HH ≥2 cm was associated with multiple worsened GERD parameters. Low LES pressure was weakly associated with an increase in the number of reflux episodes. Larger HHs, particularly >2 cm, are associated with more severe GERD parameters.
A Natural History of Patients Treated Operatively and Nonoperatively for Spinal Metastases Over 2 Years Following Treatment
Authors: Xiong Grace X. , Fisher Miles W.A. , Schwab Joseph H. , Simpson Andrew K. , Nguyen Lananh , Tobert Daniel G. , Balboni Tracy A. , Shin John H. , Ferrone Marco L. , Schoenfeld Andrew J.
Published: January 2022

Study Design.

Prospective observational study.

Objective.

We present the natural history, including survival and function, among participants in the prospective observational study of spinal metastases treatment investigation.

Summary of Background Data.

Surgical treatment has been touted as a means to preserve functional independence, quality of life, and survival. Nearly all prior investigations have been limited by retrospective design and relatively short-periods of post-treatment surveillance.

Methods.

This natural history study was conducted using the records of patients who were enrolled in the prospective observational study of spinal metastases treatment study (2017–2019). Eligible participants were 18 or older and presenting for treatment of spinal metastatic disease. Patients were followed at predetermined intervals (1, 3, 6, 12, and 24-mo) following treatment. We conducted cox proportional hazard regression analysis adjusting for confounders including age, biologic sex, number of comorbidities, type of metastatic lesion, neurologic symptoms at presentation, number of metastases involving the vertebral body, vertebral body collapse, New England Spinal Metastasis Score (NESMS) at presentation, and treatment strategy.

Results.

We included 202 patients. Twenty-three percent of the population had died by 3 months following treatment initiation, 51% by 1 year, and 70% at 2 years. There was no significant difference in survival between patients treated operatively and nonoperatively (P = 0.16). No significant difference in HRQL between groups was appreciated beyond 3 months following treatment initiation. NESMS at presentation (scores of 0 [HR 5.61; 95% CI 2.83, 11.13] and 1 [HR 3.00; 95% CI 1.60, 5.63]) was significantly associated with mortality.

Conclusion.

We found that patients treated operatively and nonoperatively for spinal metastases benefitted from treatment in terms of HRQL. Two-year mortality for the cohort as a whole was 70%. When prognosticating survival, the NESMS appears to be an effective utility, particularly among patients with scores of 0 or 1.

Level of Evidence: 2
Factors Associated with Pain Intensity and Walking Disability After Lumbar Fusion
Authors: Quek June Mei Tse , Tan Joy , Toh Irene , Chen John Li-Tat , Yeo William , Chia Rachel , Ang Adeline , Pua Yong-Hao
Published: January 2022

Study Design.

Retrospective longitudinal study.

Objective.

To identify the preoperative factors associated with postoperative lumbar fusion recovery in back or leg pain, self-reported walking time, and gait speed over a 6-month period.

Summary of Background Data.

The demand for lumbar fusion surgeries has significantly increased over the years. Yet, some patients report persistent postsurgical pain and poor functional outcomes. Unfortunately, the associated risk factors are not well understood.

Methods.

The study analyzed 232 subjects with mono- or bisegmental lumbar fusion surgery who underwent standardized assessment preoperatively and at 4, 12, and 24weeks postoperatively. Preoperative variables collected were demographic, clinical, and psychological variables. Back or leg pain was measured by the Numeric Pain Rating Scale. Walking disability was measured by self-reported walking time and performance-based fast gait speed. Risk factors of pain and walking disability over time were identified using ordinal and linear mixed-effects modeling.

Results.

At 6 months post-surgery, 17% of patients reported having moderate or severe back/leg pain and 24% were unable to walk longer than 30 minutes. Greater preoperative self-reported leg weakness frequency and body-mass-index (BMI) were strongly associated with greater pain and walking disability. Additionally, greater preoperative depression symptoms were associated with greater back/leg pain (adjusted odds ratio = 4.0) and shorter walking time (adjusted odds ratio = 2.7)—but not with slower gait speed (difference = 0.01 m/s). Old age and female gender were strongly associated with gait speed but not with self-reported walking time.

Conclusion.

A sizable proportion of patients had poor pain and walking outcomes even at 6 months post-surgery. Preoperative leg weakness and BMI were consistent risk factors and patients with greater depression symptoms may have poorer self-reported outcomes. Although requiring validation, our study has identified potentially modifiable risk factors which may give clinicians an opportunity to provide early (preoperative) and targeted intervention strategies to optimize postoperative outcomes.

Level of Evidence: NA
UNUSUAL CASE OF CLADOSPORIUM SPHAEROSPERMUM ENDOGENOUS ENDOPHTHALMITIS DURING GOLIMUMAB THERAPY: CASE REPORT AND LITERATURE REVIEW
Authors: Cavalleri Michele , Marchese Alessandro , Starace Vincenzo , Bandello Francesco , Modorati Giulio , Miserocchi Elisabetta
Published: January 2022

Purpose:

To report a case of fungal endogenous endophthalmitis from Cladosporium sphaerospermum in a patient with juvenile idiopathic arthritis receiving chronic immunosuppressive therapy with golimumab (tumor necrosis factor-α blocker).

Methods:

Case report and review of the literature.

Results:

A 34-year-old woman receiving chronic immunosuppressive therapy with golimumab for juvenile idiopathic arthritis was referred for unilateral visual loss and ocular pain. Worsening conditions after corticosteroid therapy and raised serum beta-D-glucan levels pointed to an infectious fungal etiology. Panfungal polymerase chain reaction-based genetic sequencing on vitreous specimens obtained during vitrectomy detected C. sphaerospermum. The patient management combined surgical treatment and systemic and intravitreal voriconazole.

Conclusion:

Endogenous fungal endophthalmitis can be a rare complication in patients undergoing chronic immunosuppressive therapy (including golimumab) without other predisposing factors. Prompt diagnosis and appropriate treatment are the keys to preserve vision.
A snapshot of brain and cognition in healthy mid-life and older adults
Authors: Borne Léonie , Lupton Michelle K. , Guo Christine , Mosley Philip , Adam Robert , Ceslis Amelia , Bourgeat Pierrick , Fazlollahi Amir , Maruff Paul , Rowe Christopher C. , Masters Colin L. , Fripp Jurgen , Robinson Gail A. , Breakspear Michael ,   for the Prospective Imaging Study of Ageing,   the Alzheimer’s Disease Neuroimaging Initiative,   the Australian Imaging Biomarkers and Lifestyle flagship study
Published: January 2022

Deficits in memory are seen as a canonical sign of ageing and a prodrome to dementia in older adults. However, the nature of cognitive and brain changes across a wider aperture of adulthood is not well known. We quantify the relationship between cognitive function and brain morphology from mid-life to older adulthood, and the influence of age, sex, amyloid and genetic risk for dementia. We analyzed three observational cohorts (PISA, AIBL, ADNI) with cognitive, genetic and neuroimaging measures comprising a total of 1570 healthy mid-life and older adults (mean age 72, range 49-90 years, 1330 males) and 1365 age- and sex-matched adults with mild cognitive impairment or Alzheimer’s disease. Among healthy adults, we find robust modes of co-variation between regional sulcal width and multidomain cognitive function that change from mid-life to the older age range. The most prominent cortical changes in mid-life are predominantly associated with changes in executive functions, whereas they are most strongly associated with poorer memory function in older age. These cognitive changes are accompanied by an age-dependent pattern of sulcal widening. Amyloid exerts a weak, but significant, influence on cognition, but not on sulcal width. The APOE ɛ4 allele also exerts a weak influence on cognition, but only significantly in the (larger and older) AIBL cohort. These findings provide new insights into brain and cognition in mid-life and older adults, suggesting that cognitive screening in mid-life cohorts should encompass executive functions as well as memory.
Spatial positioning and matrix programs of cancer-associated fibroblasts promote T cell exclusion in human lung tumors
Authors: Grout John A. , Sirven Philémon , Leader Andrew M. , Maskey Shrisha , Hector Eglantine , Puisieux Isabelle , Steffan Fiona , Cheng Evan , Tung Navpreet , Maurin Mathieu , Vaineau Romain , Karpf Léa , Plaud Martin , Casanova-Acebes Maria , Tabachnikova Alexandra , Keerthivasan Shilpa , Lansky Alona , LeBérichel Jessica , Walker Laura , Rahman Adeeb H. , Gnjatic Sacha , Adam Julien , Martin Jerome C. , Wolf Andrea , Flores Raja , Beasley Mary Beth , Pradhan Rachana , Müller Sören , Marron Thomas U. , Turley Shannon J. , Merad Miriam , Kenigsberg Ephraim , Salmon Hélène
Published: January 2022

It is currently accepted that activated cancer-associated fibroblasts (CAF) participate in T cell exclusion from tumor nests, but it remains unclear how they promote barrier phenotypes, and whether specific subsets are involved. Here, using single-cell RNA sequencing coupled with multiplex imaging on a large cohort of lung tumors, we identify four main CAF populations, of which only two are associated with T cell exclusion: (i) MYH11+αSMA+ CAF, which are present in early-stage tumors and form a single-cell layer lining cancer aggregates, and (ii) FAP+αSMA+ CAF, which appear in more advanced tumors and organize in patches within the stroma or in multiple layers around tumor nests. Both CAF populations show a contractility phenotype together with dense and aligned matrix fiber deposition compared to the T cell-permissive CAF. Yet they express distinct matrix genes, including COL4A1/COL9A1 (MYH11+αSMA+ CAF) and COL11A1/COL12A1 (FAP+αSMA+ CAF). Hereby, we uncovered unique molecular programs of CAF driving T cell marginalization, whose targeting should increase immunotherapy efficacy in patients bearing T cell-excluded tumors.

SIGNIFICANCE

The cellular and molecular programs driving T cell marginalization in solid tumors remain unclear. Here, we describe two CAF populations associated with T cell exclusion in human lung tumors. We demonstrate the importance of pairing molecular and spatial analysis of the tumor microenvironment, a prerequisite to develop new strategies targeting T cell-excluding CAF.
Wildlife and Marine Mammal Spatial Observatory: Observation and automated detection of Southern Right Whales in multispectral satellite imagery
Authors: Houegnigan Ludwig , Merino Enrique Romero , Vermeulen Els , Block Jessica , Safari Pooyan , Moreno-Noguer Francesc , Nadeu Climent
Published: January 2022

The Wildlife and Marine Mammal Spatial Observatory is a joint research effort for the census ofwildlife and particularly of marine mammals in satellite imagery. In that context, this paper illustrates the development of a high accuracy algorithm for the detection of right whales in sub-meter resolution multispectral satellite imagery with the constraint of a relatively small sample support of 580 southern right whale images. A significant space is devoted to exploratory data analysis to describe the statistical structure of right whale pixels and ocean surface pixels across multispectral bands.

Observations of southern right whale in satellite imagery are divided into typical and atypical right whale forms and the first observations of right whale mother and calf pairs in satellite imagery are presented. Measurements of whales are furthermore automatically extracted from whale observations (major axis length, minor axis length, etc). A significant space is also devoted to statistical data exploration, a step frequently overlooked in machine learning solutions, that yet offers interesting insight into the structure of animal detection in satellite imagery. The extracted statistics can readily be used by researchers to develop detection solutions even with low sample support. The adopted solution for detection consists of feature extraction with a convolutional neural network followed by classification with a support vector machine. 20 different convolutional neural networks were tested for feature extraction. Biostatistics parameters (accuracy, sensitivity, specificity and precision) were measured for comparison. Most architectures generally achieved high performance with low false positive and false negative rates. 100% accuracy is achieved in the case of 2 convolutional neural networks, Nasnet Large and Inception V3, and only with a specific selection of multispectral bands.

NB: This is a preprint that does not include satellite imagery due recent reviews
Does a humoral correlate of protection exist for SARS-CoV-2? A systematic review
Authors: Perry Julie , Osman Selma , Wright James , Richard-Greenblatt Melissa , Buchan Sarah A , Sadarangani Manish , Bolotin Shelly
Published: January 2022

Background

A correlate of protection (CoP) is an immunological marker associated with protection against infection. A CoP can be used to determine whether an individual is protected from infection, evaluate candidate vaccines, guide vaccination dosing intervals and policy, and understand population-level immunity against a pathogen. Despite an urgent need, a CoP for SARS-CoV-2 is currently undefined, leaving an evidence gap for informing public health policy and adapting it appropriately as new variants of concern emerge. The objective of this study was to systematically review and assess the evidence for a humoral SARS-CoV-2 CoP.

Methods and Findings

We searched OVID MEDLINE, EMBASE, Global Health, Biosis Previews and Scopus from inception to January 4, 2022 and pre-prints (using NIH iSearch COVID-19 portfolio) from inception to December 31, 2021, for studies describing SARS-CoV-2 re-infection or breakthrough infection with associated antibody measures. Two reviewers independently extracted study data and performed quality assessment. Twenty-five studies were included in our systematic review. Several studies reported re-infection or breakthrough cases that occurred in the presence of robust antibody levels. Studies that compared aggregate antibody concentrations from individuals who experienced re-infection or breakthrough compared to those who remained protected did not always find differences that were statistically significant. However, several studies found an inverse relationship between antibody levels and infection incidence, risk, or viral load, and a correlation between antibody levels and vaccine efficacy (VE). Estimates of the contribution of antibody levels to VE varied from 48.5% to 94.2%, suggesting that both humoral immunity and other immune components contribute to protection. Only two studies estimated a quantitative CoP. For Ancestral SARS-CoV-2, these included 154 (95% confidence interval (CI) 42, 559) anti-S binding antibody units/mL (BAU/mL), and 28.6% (95% CI 19.2, 29.2%) of the mean convalescent antibody level following infection. One study reported a CoP for the Alpha (B.1.1.7) variant of concern of 171 (95% CI 57, 519) BAU/mL. As of our search date, no studies reported an Omicron-specific CoP.

Conclusions

The reviewed literature was limited by a wide variation in assay methodology and antibody targets. Few studies reported SARS-CoV-2 lineage. The studies included in our review suggest that if it exists, a SARS-CoV-2 CoP is likely relative, where higher antibody levels decrease the risk of infection, but do not eliminate it completely. More work is urgently needed in this area to establish a SARS-CoV-2 CoP and guide policy as the pandemic continues.
REM sleep promotes bidirectional plasticity in developing visual cortex in vivo
Authors: Renouard Leslie , Hayworth Christopher , Rempe Michael , Clegern Will , Wisor Jonathan , Frank Marcos G.
Published: January 2022

Sleep is required for the full expression of plasticity during the visual critical period (CP). However, the precise role of rapid-eye-movement (REM) sleep in this process is undetermined. Previous studies in rodents indicate that REM sleep weakens cortical circuits following MD, but this has been explored in only one class of cortical neuron (layer 5 apical dendrites). We investigated the role of REM sleep in ocular dominance plasticity (ODP) in layer 2/3 neurons using 2-photon calcium imaging in awake CP mice. In contrast to findings in layer 5 neurons, we find that REM sleep promotes changes consistent with synaptic strengthening and weakening. This supports recent suggestions that the effects of sleep on plasticity are highly dependent upon the type of circuit and preceding waking experience.
Energetic decoupling of phycobilisomes from photosystem II involved in nonphotochemical quenching in red algae
Authors: Chiang Yu-Hao , Huang Yu-Jia , Fu Han-Yi
Published: January 2022

To mitigate photodamage under fluctuating light conditions, photosynthetic organisms respond by regulating light energy absorbed by light-harvesting complexes and used for photochemistry. Nonphotochemical quenching acts as a frontline response to prevent excitation energy from reaching the photochemical reaction center of photosystem II. The mechanisms underlying nonphotochemical quenching in red algae, which display unique combination of light-harvesting transmembrane antenna proteins and membrane-attached phycobilisomes, appear to be different from those in cyanobacteria, green algae, and plants. Several single-process models have been proposed for red algal nonphotochemical quenching, yet the possibility of more than one process being involved in nonphotochemical quenching awaits further investigation. To assess multiple nonphotochemical quenching processes in the extremophilic red alga Cyanidioschyzon merolae, fluorescence analyses with light preferentially absorbed by phycobilisomes or photosystems were utilized. Energetic decoupling of phycobilisomes from photosystem II and intrinsic photosystem II quenching were identified as two dominant processes involved in nonphotochemical quenching and distinguished by their kinetics. Whereas the degrees of energetic decoupling remained similar after its induction, the degrees of intrinsic photosystem II quenching varied depending on the illumination period and intensity. The respective effects of protein crosslinkers, osmolytes, ionophores, and photosynthetic inhibitors on the kinetics of nonphotochemical quenching suggested that the energetic decoupling involved conformational changes associated with the connection between the PBS and PSII. Furthermore, the surface charge on the thylakoid membrane played a significant role in the modulation of red algal nonphotochemical quenching.

One-sentence summary

Energetic decoupling of phycobilisomes from photosystem II and intrinsic photosystem II quenching were involved in nonphotochemical quenching of the extremophilic red alga Cyanidioschyzon merolae.
Targeting Norepinephrine Neurons of the Locus Coeruleus: A Comparison of Model Systems and Strategies
Authors: Wissing Chantal , Eschholz Lena S. , Maheu Maxime , Sauter Kathrin , Morellini Fabio , Wiegert Simon , Dieter Alexander
Published: January 2022

The locus coeruleus (LC) norepinephrine (NE) system is involved in a variety of physiological and pathophysiological processes. Refining our understanding of LC function largely relies on selective transgene expression in molecularly defined cells, allowing targeted manipulation and readout of noradrenergic neurons. Here, we performed a side-by-side comparison of the most commonly used strategies to genetically target the LC, including different cre driver lines and promoter-mediated transgene expression. We report differences between these strategies in terms of transgene expression efficacy and molecular specificity. Notably, we found no behavioral alterations in cre-expressing mice of any mouse line compared to wild-type littermates. Finally, to further facilitate the investigation of LC-NE function, we have created a suite of constructs, including reporter proteins and calcium indicators in two different spectra, whose expression is mediated by the previously described PRS×8 promoter. These constructs allow identification and monitoring of LC-NE activity either in wild-type mice, or in combination with tissue-specific manipulations of different cre driver lines. The results of our study are crucial for the interpretation of previous experiments using the respective targeting strategies, as well as for the design of future studies.

Highlights

– Heterogeneous expression patterns with different targeting strategies for LC-NE neurons

– Substantial ectopic transgene expression observed in some approaches

– No behavioral alterations in heterozygous cre mice as compared to wild-types

– PRS×8-driven reporter proteins and calcium indicators as a resource to investigate LC function
Impact of a native hemiparasite and mowing on performance of a major invasive weed, European blackberry
Authors: Cirocco Robert M. , Watling Jennifer R. , Facelli José M.
Published: January 2022

Plant invasions are a major global threat to biodiversity. Traditional methods of weed control are falling short, and novel and environmentally friendly control tools are needed. Native parasitic plants are showing promise as effective biocontrols for some of the worst weeds, however, their application is in its infancy.

First, we established the native parasitic plant, Cassytha pubescens on unmown invasive European blackberry (Rubus anglocandicans), at three field sites (Belair, Horsnell and Blackwood) in South Australia to measure the impact of infection host performance. Concurrently, we established the parasite on hosts that were mown at two of these sites (Horsnell and Blackwood), to determine the impact of mowing, a commonly used control method, in conjunction with infection by C. pubescens.

Fruit production, midday quantum yield and electron transport rates of infected R. anglocandidans were significantly lower than uninfected plants at only one site, Blackwood. Predawn quantum yield, and foliar nitrogen and phosphorus concentrations of infected plants were significantly lower than uninfected ones across all three sites. Stomatal conductance was negatively affected by infection at one site (Belair). Mowing enhanced parasite impact on host nitrogen concentration at one site (Horsnell), and infection negatively affected host stomatal conductance at the same site, irrespective of whether plants were mown or not.

We have demonstrated that this native biocontrol can be artificially established on invasive European blackberry in the field, with negative consequences for its performance. Our results demonstrate the feasibility of implementing native parasitic plants as weed biocontrols to protect biodiversity, and are aligned with the Biotic Resistance hypothesis that invasive species are susceptible and sensitive to enemies native to their newly invaded habitat.
The effector protein CgNLP1 of Colletotrichum gloeosporioides from Hevea brasiliensis disrupts nuclear localization of necrosis-induced transcription factor HbMYB8-like to suppress plant defense signaling
Authors: Yang Guangyong , Yang Jie , Zhang Qiwei , Wang Wenfeng , Feng Liping , Zhao Li , An Bang , Wang Qiannan , He Chaozu , Luo Hongli
Published: January 2022

Colletotrichum gloeosporioides is the dominant causal agent of rubber tree anthracnose and leads to serious loss of natural rubber production. Fungi secrete numerous effectors to modulate host defense systems. Understanding the molecular mechanisms by which fungal effectors regulate plant defense is of great importance for the development of novel strategies for disease control.

Here, we identified an NLP effector gene, CgNLP1, which contributed to virulence of C. gloeosporioides to rubber tree. Transient expression of CgNLP1 in the leaves of Nicotiana benthamiana induced ethylene production in plants. Ectopic expression of CgNLP1 in Arabidopsis significantly enhanced the resistance to Botrytis cinerea and A. brassicicola.

CgNLP1 was shown to target a R2R3 type transcription factor HbMYB8-like in rubber tree, which localized on nucleus and induced necrosis in N. benthamiana. CgNLP1 disrupted nuclear accumulation of HbMYB8-like and suppressed necrosis induced by HbMYB8-like mediated SA signal pathway.

This work suggested a strategy whereby C. gloeosporioides exploited CgNLP1 effector to suppress host defense to facilitate infection by disrupting the subcellular compartment of a host defense regulator HbMYB8-like.
Lipopolysaccharide induces acute lung injury and alveolar haemorrhage in association with the cytokine storm, coagulopathy and AT1R/JAK/STAT augmentation in a rat model that mimics moderate and severe Covid‐19 pathology
Authors: Al‐Ani Bahjat , ShamsEldeen Asmaa M. , Kamar Samaa S. , Haidara Mohamed A. , Al‐Hashem Fahaid , Alshahrani Mohammad Y. , Al‐Hakami Ahmed M. , Kader Dina H. Abdel , Maarouf Amro
Published: January 2022

Progress in the study of Covid‐19 disease in rodents has been hampered by the lack of angiotensin‐converting enzyme 2 (ACE2; virus entry route to the target cell) affinities for the virus spike proteins across species. Therefore, we sought to determine whether a modified protocol of lipopolysaccharide (LPS)‐induced acute respiratory distress syndrome in rats can mimic both cell signalling pathways as well as severe disease phenotypes of Covid‐19 disease. Rats were injected via intratracheal (IT) instillation with either 15 mg/kg of LPS (model group) or saline (control group) before being killed after 3 days. A severe acute respiratory syndrome (SARS)‐like effect was observed in the model group as demonstrated by the development of a “cytokine storm” (>2.7 fold increase in blood levels of IL‐6, IL‐17A, GM‐CSF, and TNF‐α), high blood ferritin, demonstrable coagulopathy, including elevated D‐dimer (approximately 10‐fold increase), PAI‐1, PT, and APTT (p < 0.0001). In addition, LPS increased the expression of lung angiotensin II type I receptor (AT1R)‐JAK‐STAT axis (>4 fold increase). Chest imaging revealed bilateral small patchy opacities of the lungs. Severe lung injury was noted by the presence of both, alveolar collapse and haemorrhage, desquamation of epithelial cells in the airway lumen, infiltration of inflammatory cells (CD45+ leukocytes), widespread thickening of the interalveolar septa, and ultrastructural alterations similar to Covid‐19. Thus, these findings demonstrate that IT injection of 15 mg/kg LPS into rats, induced an AT1R/JAK/STAT‐mediated cytokine storm with resultant pneumonia and coagulopathy that was commensurate with moderate and severe Covid‐19 disease noted in humans.
Salt loading with unilateral nephrectomy accelerates decline in glomerular filtration rate in the hypertensive, obese, type 2 diabetic SDT fatty rat model of diabetic kidney disease
Authors: Shinozaki Yuichi , Katayama Yuko , Yamaguchi Fuminari , Suzuki Tomohisa , Watanabe Kana , Uno Kinuko , Tsutsui Takahiro , Sugimoto Miki , Shinohara Masami , Miyajima Katsuhiro , Ohta Takeshi
Published: January 2022

For the evaluation of novel therapeutic agents for diabetic kidney disease (DKD), it is desirable to examine their efficacy in animal models by using the glomerular filtration rate (GFR) as an index. For this purpose, animal models that demonstrate a short‐term GFR decline because of disease progression are required. Therefore, we aimed to develop such an animal model of DKD by using obese type 2 diabetic spontaneously diabetic Torii (SDT) fatty rats treated with salt loading by drinking water containing sodium chloride with or without unilateral nephrectomy. As a result, we have found that 0.3% salt loading with unilateral nephrectomy or 0.8% salt loading alone caused a rapid GFR decline, hypertension and rapid development of tubulointerstitial fibrosis. Moreover, the addition of losartan to a mixed diet suppressed the GFR decline in SDT fatty rats treated with 0.3% salt loading with unilateral nephrectomy. These results suggest that the model of SDT fatty rats treated with 0.3% salt loading and unilateral nephrectomy could be used as a hypertensive DKD model for evaluating therapeutic agents based on suppression of GFR decline.
Transdermal sensor features correlate with ecological momentary assessment drinking reports and predict alcohol‐related consequences in young adults’ natural settings
Authors: Russell Michael A. , Turrisi Robert J. , Smyth Joshua M.
Published: January 2022

Background

Wearable transdermal alcohol concentration (TAC) sensors allow passive monitoring of alcohol concentration in natural settings and measurement of multiple features from drinking episodes, including peak intoxication level, speed of intoxication (absorption rate) and elimination, and duration. These passively collected features extend commonly used self‐reported drink counts and may facilitate the prediction of alcohol‐related consequences in natural settings, aiding risk stratification and prevention efforts.

Method

A total of 222 young adults aged 21–29 (M age = 22.3, 64% female, 79% non‐Hispanic white, 84% undergraduates) who regularly drink heavily participated in a 5‐day study that included the ecological momentary assessment (EMA) of alcohol consumption (daily morning reports and participant‐initiated episodic EMA sequences) and the wearing of TAC sensors (SCRAM‐CAM anklets). The analytic sample contained 218 participants and 1274 days (including 554 self‐reported drinking days). Five features—area under the curve (AUC), peak TAC, rise rate (rate of absorption), fall rate (rate of elimination), and duration—were extracted from TAC‐positive trajectories for each drinking day. Day‐ and person‐level associations of TAC features with drink counts (morning and episodic EMA) and alcohol‐related consequences were tested using multilevel modeling.

Results

TAC features were strongly associated with morning drink reports (r = 0.6–0.7) but only moderately associated with episodic EMA drink counts (r = 0.3–0.5) at both day and person levels. Higher peaks, larger AUCs, faster rise rates, and faster fall rates were significantly predictive of day‐level alcohol‐related consequences after adjusting for both morning and episodic EMA drink counts in separate models. Person means of TAC features added little above daily scores to the prediction of alcohol‐related consequences.

Conclusions

These results support the utility of TAC sensors in studies of alcohol misuse among young adults in natural settings and outline the specific TAC features that contribute to the day‐level prediction of alcohol‐related consequences. TAC sensors provide a passive option for obtaining valid and unique information predictive of drinking risk in natural settings.
The role of surgery in weaning patients from home parenteral support – A cohort study
Authors: McKee Ruth F. , Knight Katrina , Leitch E. Fiona , Stevens Phil
Published: January 2022

Aim

Some patients with intestinal failure requiring home parenteral support (HPS) may be weaned. This study considered all abdominal surgery in a cohort of HPS patients over a 25‐year period. Our aim was to identify how many patients can be weaned from HPS and by what means, and to identify what makes weaning more likely.

Method

A prospectively collected database of HPS patients to December 2018 was analysed for outcomes of care.

Results

At 5 years 56% of 205 patients remained on HPS. Fifty eight patients (28%), who had 68 operations, stopped HPS after surgery. Patients stopping HPS had a longer median final small bowel length (155 cm, range 45–350 cm) and were more likely to have colon in circuit (84%) than patients who had reconstructive surgery but did not stop HPS (median small bowel length 50 cm, range 15–135 cm; 50% colon in circuit). The median period between HPS discharge and reconstructive surgery was 238 days. There were no deaths, but 18 Clavien–Dindo grade 3–4 complications occurred within 30 days. Ninety per cent of patients who stopped HPS survived for 5 years from the start of HPS in comparison with 53% of those who remained on HPS.

Conclusions

No previous study has examined surgery in an entire cohort of HPS patients. More than a quarter of HPS patients can be weaned after reconstructive surgery. The length of bowel available for recruitment at surgery is the main determinant of the ability to stop HPS. The possibility of reconstruction should be considered, since patients who stop HPS appear to have a survival advantage.
Elucidating the Common Basis for Task‐Dependent Differential Manifestations of Category Advantage: A Decision Theoretic Approach
Authors: Akbiyik Seda , Göksun Tilbe , Balcı Fuat
Published: January 2022

Cross‐category hues are differentiated easier than otherwise equidistant hues that belong to the same linguistic category. This effect is typically manifested through both accuracy and response time gains in tasks with a memory component, whereas only response times are affected when there is no memory component. This raises the question of whether there is a common generative process underlying the differential behavioral manifestations of category advantage in color perception. For instance, within the framework of noisy evidence accumulation models, changes in accuracy can be readily attributed to an increase in the efficacy of perceptual evidence integration (after controlling for threshold setting), whereas changes in response time can also be attributed to shorter nondecisional delays (e.g., due to facilitated signal detection). To address the latent decision processes underlying category advantage across different behavioral demands, we introduce a decision‐theoretic perspective (i.e., diffusion decision model) to categorical color perception in three complementary experiments. In Experiment 1, we collected data from a binary color naming task (1) to determine the green–blue boundary in our sample and (2) to trace how parameter estimates of interest in the model output change as a function of color typicality. In Experiments 2 and 3, we used same‐different task paradigms (with and without a memory component, respectively) and traced the category advantage in color discrimination in two parameters of the diffusion decision model: nondecision time and drift rate. An increase in drift rate predominantly characterized the category advantage in both tasks. Our results show that improved efficiency in perceptual evidence integration is a common driving force behind different manifestations of category advantage.
The Power of Ignoring: Filtering Input for Argument Structure Acquisition
Authors: Perkins Laurel , Feldman Naomi H. , Lidz Jeffrey
Published: January 2022

Learning in any domain depends on how the data for learning are represented. In the domain of language acquisition, children's representations of the speech they hear determine what generalizations they can draw about their target grammar. But these input representations change over development as a function of children's developing linguistic knowledge, and may be incomplete or inaccurate when children lack the knowledge to parse their input veridically. How does learning succeed in the face of potentially misleading data? We address this issue using the case study of “non‐basic” clauses in verb learning. A young infant hearing What did Amy fix? might not recognize that what stands in for the direct object of fix, and might think that fix is occurring without a direct object. We follow a previous proposal that children might filter nonbasic clauses out of the data for learning verb argument structure, but offer a new approach. Instead of assuming that children identify the data to filter in advance, we demonstrate computationally that it is possible for learners to infer a filter on their input without knowing which clauses are nonbasic. We instantiate a learner that considers the possibility that it misparses some of the sentences it hears, and learns to filter out those parsing errors in order to correctly infer transitivity for the majority of 50 frequent verbs in child‐directed speech. Our learner offers a novel solution to the problem of learning from immature input representations: Learners may be able to avoid drawing faulty inferences from misleading data by identifying a filter on their input, without knowing in advance what needs to be filtered.
Hierarchical Integration of Communicative and Spatial Perspective‐Taking Demands in Sensorimotor Control of Referential Pointing
Authors: Liu（刘） Rui（睿） , Bögels Sara , Bird Geoffrey , Medendorp W. Pieter , Toni Ivan
Published: January 2022

Recognized as a simple communicative behavior, referential pointing is cognitively complex because it invites a communicator to consider an addressee's knowledge. Although we know referential pointing is affected by addressees’ physical location, it remains unclear whether and how communicators’ inferences about addressees’ mental representation of the interaction space influence sensorimotor control of referential pointing. The communicative perspective‐taking task requires a communicator to point at one out of multiple referents either to instruct an addressee which one should be selected (communicative, COM) or to predict which one the addressee will select (non‐communicative, NCOM), based on either which referents can be seen (Level‐1 perspective‐taking, PT1) or how the referents were perceived (Level‐2 perspective‐taking, PT2) by the addressee. Communicators took longer to initiate the movements in PT2 than PT1 trials, and they held their pointing fingers for longer at the referent in COM than NCOM trials. The novel findings of this study pertain to trajectory control of the pointing movements. Increasing both communicative and perspective‐taking demands led to longer pointing trajectories, with an under‐additive interaction between those two experimental factors. This finding suggests that participants generate communicative behaviors that are as informative as required rather than overly exaggerated displays, by integrating communicative and perspective‐taking information hierarchically during sensorimotor control. This observation has consequences for models of human communication. It implies that the format of communicative and perspective‐taking knowledge needs to be commensurate with the movement dynamics controlled by the sensorimotor system.
Infants’ Attributions of Insides and Animacy in Causal Interactions
Authors: Kominsky Jonathan F. , Li Yiping , Carey Susan
Published: January 2022

Past work has found that infants show more interest when an object that has at least two properties of animate beings, such as engaging in self‐generated motion and having fur, is shown to be hollow than when an object with none or one of these properties is revealed to be hollow. When an object is grabbed by a hand and moved to a new place, by 7 months of age, infants explain the motion of the object as due to the hand, and thus do not interpret this object as capable of self‐generated motion. This constant application of force is called an “entraining” event. Other work has found that 6‐month‐old infants are sensitive to the reversals of causal roles in “launching” events (billiard‐ball‐like collisions), but not entraining events. Here, we examine whether 10‐month‐old infants explain the motion of the patient in a launching event as being due to the contact with the launching agent. Experiment 1 replicates past work, showing that infants look longer when a self‐propelled object with animate features (fur or feathers) is shown to be hollow, compared to a similar object undergoing spatiotemporally identical motion entrained by a human agent. Experiment 2 finds that infants look equally at the agent and patient, both covered by fur or feathers, of a launching event when each is revealed to be hollow. Experiment 3 shows that infants look longer when a fur‐covered causal patient is shown to be hollow compared to a plain‐box causal agent, indicating that 10‐month‐old infants do not explain the motion of the causal patient of a launching event as due to the agent, even though they do so for an entraining event. This dissociation suggests the existence of multiple independent causal representations in the first year of life.