julilili42/papers huggingface dataset:
Botrytis cinereainfection accelerates ripening and cell wall disassembly to promote disease in tomato fruit
2022-09-02

Abstract Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease in tomato (Solanum lycopersicum). Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an enzyme-linked immunosorbent assay (ELISA)-based glycomics technique used to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening depends on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbc polygalacturonase1 Δbc polygalacturonase2 lacking two critical pectin degrading enzymes was incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.
Autoreactive napsin A–specific T cells are enriched in lung tumors and inflammatory lung lesions during immune checkpoint blockade
2022-09-02

Cancer treatment with immune checkpoint blockade (ICB) often induces immune-related adverse events (irAEs). We hypothesized that proteins coexpressed in tumors and normal cells could be antigenic targets in irAEs and herein described DITAS (discovery of tumor-associated self-antigens) for their identification. DITAS computed transcriptional similarity between lung tumors and healthy lung tissue based on single-sample gene set enrichment analysis. This identified 10 lung tissue–specific genes highly expressed in the lung tumors. Computational analysis was combined with functional T cell assays and single-cell RNA sequencing of the antigen-specific T cells to validate the lung tumor self-antigens. In patients with non–small cell lung cancer (NSCLC) treated with ICB, napsin A was a self-antigen that elicited strong CD8 + T cell responses, with ICB responders harboring higher frequencies of these CD8 + T cells compared with nonresponders. Human leukocyte antigen (HLA) class I ligands derived from napsin A were present in human lung tumors and in nontumor lung tissues, and napsin A tetramers confirmed the presence of napsin A–specific CD8 + T cells in blood and tumors of patients with NSCLC. Napsin A–specific T cell clonotypes were enriched in lung tumors and ICB-induced inflammatory lung lesions and could kill immortalized HLA-matched NSCLC cells ex vivo. Single-cell RNA sequencing revealed that these T cell clonotypes expressed proinflammatory cytokines and cytotoxic markers. Thus, DITAS successfully identified self-antigens, including napsin A, that likely mediate effective antitumor T cell responses in NSCLC and may simultaneously underpin lung irAEs.
The enhanced x-ray timing and polarimetry mission: eXTP: an update on its scientific cases, mission profile and development status
2022-09-02

&lt;p&gt;The enhanced X-ray Timing and Polarimetry mission (eXTP) is a flagship observatory for X-ray timing, spectroscopy and polarimetry developed by an International Consortium. Thanks to its very large collecting area, good spectral resolution and unprecedented polarimetry capabilities, eXTP will explore the properties of matter and the propagation of light in the most extreme conditions found in the Universe. eXTP will, in addition, be a powerful X-ray observatory. The mission will continuously monitor the X-ray sky, and will enable multi-wavelength and multi-messenger studies. The mission is currently in phase B, which will be completed in the middle of 2022.&lt;/p&gt;
Dual near‐infrared II laser modulates the cellular redox state of T cells and augments the efficacy of cancer immunotherapy
2022-09-02

Abstract Immunotherapy, including immune checkpoint inhibitors, has revolutionized cancer treatment, but only a minor fraction of patients shows durable responses. A new approach to overcome this limitation is yet to be identified. Recently, we have shown that photobiomodulation (PBM) with near‐infrared (NIR) light in the NIR‐II window reduces oxidative stress and supports the proliferation of CD8 + T cells, suggesting that PBM with NIR‐II light could augment anti‐cancer immunity. Here, we report a novel approach to support tumor‐infiltrating CD8 + T cells upon PBM with NIR‐II laser with high tissue penetration depth. Brief treatments of a murine model of breast cancer with dual 1064 and 1270 nm lasers reduced the expression of the programmed cell death protein 1 (PD‐1) in CD8 + T cells in a syngeneic mouse model of breast cancer. The direct effect of the NIR‐II laser treatment on T cells was confirmed by the enhanced tumor growth delay by the adoptive transfer of laser‐treated CD8 + T cells ex vivo against a model tumor antigen. We further demonstrated that specific NIR‐II laser parameters augmented the effect of the immune checkpoint inhibitor on tumor growth. PBM with NIR‐II light augments the efficacy of cancer immunotherapy by supporting CD8 + T cells. Unlike the current immunotherapy with risks of undesirable drug–drug interactions and severe adverse events, the laser is safe and low‐cost. It can be broadly combined with other therapy without modification to achieve clinical significance. In addition, our study established a path to develop a novel laser‐based therapy to treat cancer effectively.
No evidence for age-related alterations in the marmoset retina
2022-09-02

The physiological aging process of the retina is accompanied by various and sometimes extensive changes: Macular degeneration, retinopathies and glaucoma are the most common findings in the elderly and can potentially lead to irreversible visual disablements up to blindness. To study the aging process and to identify possible therapeutic targets to counteract these diseases, the use of appropriate animal models is mandatory. Besides the most commonly used rodent species, a non-human primate, the common marmoset ( Callithrix jacchus ) emerged as a promising animal model of human aging over the last years. However, the visual aging process in this species is only partially characterized, especially with regard to retinal aberrations. Therefore, we assessed here for the first time potential changes in retinal morphology of the common marmoset of different age groups. By cell type specific immunolabeling, we analyzed different cell types and distributions, potential photoreceptor and ganglion cell loss, and structural reorganization. We detected no signs of age-related differences in staining patterns or densities of various cell populations. For example, there were no signs of photoreceptor degeneration, and there was only minimal sprouting of rod bipolar cells in aged retinas. Altogether, we describe here the maintenance of a stable neuronal architecture, distribution and number of different cell populations with only mild aberrations during the aging process in the common marmoset retina. These findings are in stark contrast to previously reported findings in rodent species and humans and deserve further investigations to identify the underlying mechanisms and possible therapeutic targets.
Subsistence practices in Phoenicia and beyond: faunal investigations at Tell el-Burak, Lebanon (c. 725–350 BCE)
2022-09-02

Agricultural practices in Iron Age Phoenicia are an understudied field of research. The most recently excavated faunal evidence from Tell el-Burak, a coastal agricultural domain linked to either Sidon or Sarepta, will increase our understanding of this topic. This paper provides the first diachronic and detailed analysis of the Late Iron Age and Persian period faunal data from Tell el-Burak, and investigates the subsistence practices of its people during the late 8th to mid-4th centuries BCE. The diet of its inhabitants mainly consists of caprines, while a high percentage of donkeys and cattle remains coincide with the peak of winemaking activities at the site. The results from Tell el-Burak are then compared with faunal data from other sites in the territory traditionally known as Phoenicia, as well as with faunal data from the neighbouring regions of the Levant. The comparisons show differences between the northern and southern Levant and similarities between southern Phoenicia and the southern Levant.
Perioperative diagnosis and impact of acquired von Willebrand syndrome in infants with congenital heart disease
2022-09-02

Abstract Acquired von Willebrand syndrome (aVWS) has been reported in patients with congenital heart diseases associated with shear stress caused by significant blood flow gradients. Its etiology and impact on intraoperative bleeding during pediatric cardiac surgery have not been systematically studied. This single-center, prospective, observational study investigated appropriate diagnostic tools of aVWS compared with multimer analysis as diagnostic criterion standard and aimed to clarify the role of aVWS in intraoperative hemorrhage. A total of 65 newborns and infants aged 0 to 12 months scheduled for cardiac surgery at our tertiary referral center from March 2018 to July 2019 were included in the analysis. The glycoprotein Ib M assay (GPIbM)/von Willebrand factor antigen (VWF:Ag) ratio provided the best predictability of aVWS (area under the receiver operating characteristic curve [AUC], 0.81 [95% CI, 0.75-0.86]), followed by VWF collagen binding assay/VWF:Ag ratio (AUC, 0.70 [0.63-0.77]) and peak systolic echocardiographic gradients (AUC, 0.69 [0.62-0.76]). A cutoff value of 0.83 was proposed for the GPIbM/VWF:Ag ratio. Intraoperative high-molecular-weight multimer ratios were inversely correlated with cardiopulmonary bypass (CPB) time (r = −0.57) and aortic cross-clamp time (r = −0.54). Patients with intraoperative aVWS received significantly more fresh frozen plasma (P = .016) and fibrinogen concentrate (P = .011) than those without. The amounts of other administered blood components and chest closure times did not differ significantly. CPB appears to trigger aVWS in pediatric cardiac surgery. The GPIbM/VWF:Ag ratio is a reliable test that can be included in routine intraoperative laboratory workup. Our data provide the basis for further studies in larger patient cohorts to achieve definitive clarification of the effects of aVWS and its potential treatment on intraoperative bleeding.
Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation
2022-09-02

Natural-abundance measurements of nitrate and nitrite (NO x ) isotope ratios (δ 15 N and δ 18 O) can be a valuable tool to study the biogeochemical fate of NO x species in the environment. A prerequisite for using NO x isotopes in this regard is an understanding of the mechanistic details of isotope fractionation ( 15 ε, 18 ε) associated with the biotic and abiotic NO x transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NO x reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO 3 – ) and nitrite (NO 2 – ) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that 15 ε and 18 ε values obtained for heterotrophic ( 15 ε-NO 3 – : 17.6 ± 2.8‰, 18 ε-NO 3 – :18.1 ± 2.5‰; 15 ε-NO 2 – : 14.4 ± 3.2‰) vs. mixotrophic ( 15 ε-NO 3 – : 20.2 ± 1.4‰, 18 ε-NO 3 – : 19.5 ± 1.5‰; 15 ε-NO 2 – : 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NO x reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics ( 15 ε-NO 2 – : –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NO x reduction. The similar isotope effects detected during mixotrophic and heterotrophic NO x reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NO x reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.
Advances in non-invasive tracking of wave-type electric fish in natural and laboratory settings
2022-09-02

Recent technological advances greatly improved the possibility to study freely behaving animals in natural conditions. However, many systems still rely on animal-mounted devices, which can already bias behavioral observations. Alternatively, animal behaviors can be detected and tracked in recordings of stationary sensors, e.g., video cameras. While these approaches circumvent the influence of animal-mounted devices, identification of individuals is much more challenging. We take advantage of the individual-specific electric fields electric fish generate by discharging their electric organ (EOD) to record and track their movement and communication behaviors without interfering with the animals themselves. EODs of complete groups of fish can be recorded with electrode arrays submerged in the water and then be tracked for individual fish. Here, we present an improved algorithm for tracking electric signals of wave-type electric fish. Our algorithm benefits from combining and refining previous approaches of tracking individual specific EOD frequencies and spatial electric field properties. In this process, the similarity of signal pairs in extended data windows determines their tracking order, making the algorithm more robust against detection losses and intersections. We quantify the performance of the algorithm and show its application for a data set recorded with an array of 64 electrodes distributed over a 12 m 2 section of a stream in the Llanos, Colombia, where we managed, for the first time, to track Apteronotus leptorhynchus over many days. These technological advances make electric fish a unique model system for a detailed analysis of social and communication behaviors, with strong implications for our research on sensory coding.
Does an experimentally induced self-association elicit affective self-prioritisation?
2022-09-02

Self-relevant stimuli such as one’s name and face have been demonstrated to influence information processing in both the cognitive and affective domains. It has been observed that recently self-associated stimuli can also influence cognition, but their impact on affect has not been tested yet. In the current study ( N = 107), we test whether recently self-associated stimuli yield an affective bias and compare the size of the effect with that of familiar self-associated stimuli. A Recoding-Free Implicit Association Test (IAT-RF) presenting self-associated, neutral object-associated, positive, and negative stimuli was used with two groups: one which categorised familiar words as self- and neutral object-associated stimuli, and a second which categorised recently self- and neutral object-associated geometric shapes. In both cases, response times were faster for congruent trials, which mapped response keys as “positive/self” and “negative/neutral object,” than for incongruent trials which mapped response keys as “positive/neutral object” and “negative/self.” The size of the effect yielded by familiar and new self-associated stimuli did not differ. This indicates that experimentally induced self-association can immediately yield an affective bias in favour of the self-associated stimulus.
Using authentic representations of practice in teacher education: Do direct instructional and problem-based approaches really produce different effects?
2022-09-02

This paper investigates the effects of different instructional approaches (problem-based vs. direct instructional) on student teachers‘ analysis of practice when using authentic representations of practice in teacher education. We assigned 638 student teachers from 21 equivalent teacher education courses to one of the two conditions. Students’ analyses of practice were evaluated on selective attention, reflective thought, and theory-practice integrations in a pre-post-design. In line with inconsistent findings from prior research, we were able to produce evidence for equivalent effects of the instructional approaches on all dependent variables using Bayesian data analyses. As called for in a review on the topic, we additionally explored the role of the instructors administering the field study interventions. Findings revealed that a positive attitude toward the instructional approach the instructors administered was related to more theory-practice integrations in the students’ analyses.
Humoral antimalaria immune response in Nigerian children exposed to helminth and malaria parasites
2022-09-02

Background Malaria and helminthic parasites are endemic in tropical countries, and co-infections might influence host-parasite interactions. In this community-based cross-sectional study, the effect that the presence of soil-transmitted helminths (STH) (Hookworm, Hymenolepis nana) and Schistosoma haematobium infections could have on the immunoglobulin (Ig) candidate protein of the malaria vaccine GMZ2 levels was evaluated. Methods Blood, stool, and urine samples were collected from 5-15-year-old children to diagnose P. falciparum (Pf), STH, and Schistosoma haematobium , respectively. Identification and quantification of the parasite load of STH and S. haematobium were achieved by light microscopy. A polymerase chain reaction was carried out to detect submicroscopic infections of P. falciparum . Plasma levels of GMZ2 specific IgG and its subclasses were quantified by ELISA. Results The median level of total IgG in individuals with co-infection with Pf/ H . nana was significantly lower in the mono-infected group with Pf (p = 0.0121) or study participants without infection ( p =0.0217). Similarly, the median level of IgG1 was statistically lower in Pf/ H. nana group compared to Pf-group ( p =0.0137). Equally, the Pf/ H. nana infected individuals posted a lower level of IgG1 compared to Pf-group (p=0.0137) and IgG4 compared to the Pf-group ( p =0.0144). Spearman rank correlation analyses indicated positive relationships between the densities of H. nana (ρ=0.25, p =0.015) and S. haematobium (ρ=0.36, p&amp;lt; 0.0001). Conclusions Hookworm and H. nana infections are associated with reduced GMZ2 specific IgG levels. This study shows the possible manipulation of immune responses by helminths for their survival and transmission, which may have serious implications for vaccine development and deployment in helminth-endemic regions.
Self-organizing morphogenetic mechanisms as processors of evolution.
2022-09-02

Many organismic shapes and ornamentations are analogous to self-organizing patterns in the non-biological world. lt is suggested that responsible processes become first serendipitously "adopted" by developmental systems and then "lamed" by Darwinian selection as soon as a specific function has been acquired. Yet, taming can only reduce, bul not eliminare, the unpredictability of the dynamic systems at the local level.
The effect of hunger state on hypothalamic functional connectivity in response to food cues
2022-09-03

Abstract The neural underpinnings of the integration of internal and external cues that reflect nutritional status are poorly understood in humans. The hypothalamus is a key integrative area involved in short‐ and long‐term energy intake regulation. Hence, we examined the effect of hunger state on the hypothalamus network using functional magnetic resonance imaging. In a multicenter study, participants performed a food cue viewing task either fasted or sated on two separate days. We evaluated hypothalamic functional connectivity (FC) using psychophysiological interactions during high versus low caloric food cue viewing in 107 adults (divided into four groups based on age and body mass index [BMI]; age range 24–76 years; BMI range 19.5–41.5 kg/m 2 ). In the sated compared to the fasted condition, the hypothalamus showed significantly higher FC with the bilateral caudate, the left insula and parts of the left inferior frontal cortex. Interestingly, we observed a significant interaction between hunger state and BMI group in the dorsolateral prefrontal cortex (DLPFC). Participants with normal weight compared to overweight and obesity showed higher FC between the hypothalamus and DLPFC in the fasted condition. The current study showed that task‐based FC of the hypothalamus can be modulated by internal (hunger state) and external cues (i.e., food cues with varying caloric content) with a general enhanced communication in the sated state and obesity‐associated differences in hypothalamus to DLPFC communication. This could potentially promote overeating in persons with obesity.
ex vivo–in vivo comparison of drug penetration analysis by confocal Raman microspectroscopy and tape stripping
2022-09-03

Abstract When it comes to skin penetration analysis of a topically applied formulation, the number of suitable methods is limited, and they often lack in spatial resolution. In vivo studies are pivotal, especially in the approval of a new product, but high costs and ethical difficulties are limiting factors. For that reason, good ex vivo models for testing skin penetration are crucial. In this study, caffeine was used as a hydrophilic model drug, applied as a 2% (w/w) hydrogel, to compare different techniques for skin penetration analysis. Confocal Raman microspectroscopy (CRM) and tape stripping with subsequent HPLC analysis were used to quantify caffeine. Experiments were performed ex vivo and in vivo. Furthermore, the effect of 5% (w/w) 1,2‐pentanediol on caffeine skin penetration was tested, to compare those methods regarding their effectiveness in detecting differences between both formulations.