Miracle-dz/UniFAR-FTUs huggingface dataset:
Mirror-Image Lesions in Sequential Relapses of AQP4-Positive Neuromyelitis Optica Spectrum Disorder

A 25 year-old Nigerian woman with aquaporin-4 antibody-positive neuromyelitis optica spectrum disorder (NMOSD) presented with a 6 week history of nausea, vomiting, and refractory hiccups; as well as progressive lower extremity sensory loss, weakness, saddle anesthesia, and urinary incontinence. She had experienced her first NMOSD relapse seven years prior with bilateral lower extremity weakness and area postrema syndrome. After pulse steroids and plasma exchange she made a complete neurologic recovery and was started on azathioprine. An initial aquaporin-4 (AQP4) antibody ELISA test was positive, but three subsequent tests were negative and repeat MRI brain showed resolution of T2/FLAIR signal abnormalities with the exception of a right thalamic lesion and a left medullary lesion. Azathioprine was discontinued after 1 year and she was lost to follow-up. With her second relapse, she had new lesions in her left thalamus and right medulla—a mirror image of the thalamic and medullary lesions associated with her first relapse. In addition, an MRI spine demonstrated a new longitudinally extensive transverse myelitis from T7 to L1 with edematous expansion of the cord. Her serum AQP4 antibody test using a cell-based assay was strongly positive. NMOSD lesions are typically associated with brain regions with high density of the AQP4 channel. These areas include optic nerves, hypothalamus, and the diencephalic and brainstem tissues that surround the cerebral aqueduct and third and fourth ventricles. Previous studies have demonstrated that those with relapsing NMOSD have a predilection for recurrence in the same neuroanatomical region as their first episode. We hypothesize, using data from prior pathologic and epidemiologic studies, that mirror image lesions, where the same anatomic sites are affected on the contralateral side of the brain or spinal cord, may appear in subsequent attacks due to (i) areas of high remaining AQP4 density and/or (ii) local compromise of astrocyte or blood-brain barrier (BBB) function that persists after the initial inciting attack.
Impact of Soybean Nodulation Phenotypes and Nitrogen Fertilizer Levels on the Rhizosphere Bacterial Community

The effects of nodulation properties of legumes on the rhizosphere bacterial community are still not clear. To determine the effects of nodulation phenotypes on bacterial communities in the rhizosphere of soybean plants, we performed high-throughput sequencing of the 16S rRNA gene to estimate the rhizosphere bacterial community of three soybean lines with different nodulation phenotypes grown in soil supplied with different levels of N fertilizer. The results revealed that both the soybean nodulation phenotypes and the N levels affected the rhizosphere bacteria community, but the nodulation phenotypes contributed more than the N-supply. The diversity of bacteria was decreased in the rhizosphere of super-nodulating phenotype. The response of rhizosphere bacterial communities to the soil available nitrogen (AN) concentrations was different than the response with the three nodulation phenotypes of soybean which was more stable in the wild-type (Nod+) soybean samples than that in the mutant samples (Nod– and Nod++). Bradyrhizobium in the rhizosphere was positively correlated with nodule number and negatively correlated to AN in the soil, while Burkholderia and Dyella were positively correlated with nodule biomass and nitrogenase activity. These results demonstrated that the nodulation phenotype of soybean affects the rhizosphere microbiome.
How Much Is 2 × 4? Understanding How the Brain Solves Arithmetic Problems

How much is 2 × 4? Sounds like an easy question, but have you ever thought about how you solve that problem? In this article you will learn about two different strategies that we use to solve arithmetic problems. You will also get to know the different brain areas—like the intraparietal sulcus—that work together when you use these different strategies. Which strategy and which brain regions you use changes over time as you get more familiar with arithmetic. This transition is especially visible in the way brain areas work and communicate with one another—some areas become more active, while others become less active. After reading this article, you will know more about the techniques we use to solve arithmetic problems and the brain areas needed to find the answers for your next math homework assignment.
Impact of the production method and diagnostics conditions on the compositions and structure of nanodimensional anatase

Abstract The detail investigation of the samples with nanodimensional anatase, formed by hydrolysis of TiOSO4 × xH2O without or in the presence of polymer poly(N-vinyl caprolactam), physical precipitation of the polymer followed by the capture of commercial Hombifine N are performed by X-ray powder diffraction using laboratory and synchrotron radiation sources, transmission electron microscopy with the diffraction, and elemental analysis. The two «core»-«shell» models with nanoparticles and their associates as a core can be applied to samples produced. The synchrotron and electron radiation change the degree of crystallinity and the imperfection of anatase, isolate of TiO2−x(OH)2x × yH2O from the nanoparticle shell with a decrease in its thickness, lead to the anatase – rutile phase transition. The double diffraction effect on the appearance of kinematically forbidden reflections caused by the dynamic character of the electron diffraction. The photoactivity depends on microstructural characteristics (specific surface, nanoobjects sizes). The structure and elemental composition of nanoparticles (associates) affect antimicrobial activity against Staphylococcus aureus and Escherichia coli.
Differential expression of multiple PR10 proteins in western white pine following wounding, fungal infection and cold-hardening

Herein the wound-induced expression of a set of PR10 genes (PmPR10) from Pinus monticola (Dougl. Ex D. Don) is described. Thirteen different PmPR10 cDNAs were isolated and their nucleotide sequences were determined from wounded needles. Northern blot analysis showed that PmPR10 gene expression was activated with both local and systemic responses after wounding, and the accumulation of PmPR10 transcript was much more abundant and rapid in wounded needles than in unwounded tissues. Western immunoblot analysis demonstrated that PmPR10 protein synthesis was activated upon wounding, suggesting that the expression of the wound-activated PmPR10 gene was regulated at the transcription level. In wounded needles, the PR10 protein level increased from day 1 to day 8 after treatment. Western immunoblot analysis following isoelectric focusing and two-dimensional electrophoresis revealed that nine PmPR10 proteins accumulated to different extents after wounding. These proteins have a molecular mass of about 18 kDa with different isoelectrical points ranging from 5.2 to 6.0. Wound-inducible PmPR10 proteins were differentially expressed in response to cold-hardening and fungal infection. The wound-induced PmPR10 protein accumulation was enhanced by the wound-signal compound methyl jasmonate and okadaic acid, a specific inhibitor of type 1 or type 2 A serine/threonine protein phosphatases. However, it was partially suppressed by salicylic acid and abscisic acid. These data provide an opportunity to elucidate further the signal transduction pathway involved in the activation of PmPR10 protein synthesis in the defence response of white pine against mechanical injury.
“To have or not to have a boyfriend?” Large identities in small stories

Abstract In this paper, I draw on recent work on small stories that has been proposed as a counter-move to the dominant paradigm of big stories. Small stories are fragmented, heavily co-authored and open-ended tellings, and have proved a prime site for the joint drafting of identity positions in concrete interactional sites. The context in which the use of small stories is examined in this study is a group of three 20-year-old Greek women, who portray themselves as best friends. This friendship group was studied ethnographically in Syros (Greece) between 2014 and 2015, and data collection involved 10 hours of audio-recorded conversations, as well as field-notes. For the analysis of the participants’ small stories, this paper draws on positioning analysis and conversation analysis vis-à-vis small stories research as a framework to study identities-in-interaction. In particular, it employs the model of positioning in the fine-grained micro-analysis of a co-authored ‘small story’ about relationships with men. It demonstrates how the deferrals of telling and the refusals to tell are as integral a part of the analysis as the actual telling, since they allow us insights into the teller’s contradictory views about big issues and large identities. Moreover, the findings show how the teller manages the participation framework in cases of narrating difficult topics and ambivalent identities.
Antibiosis component of resistance in sorghum to sorghum midge, Contarinia sorghicola

SUMMARY Sorghum midge, Contarinia sorghicola Coq. (Diptera: Cecidomyiidae) is an important pest of grain sorghum, and host-plant resistance is one of the most effective means of controlling this pest. We studied the antibiosis mechanism of resistance in sorghum to C. sorghicola in a diverse array of midge-resistant and midge-susceptible genotypes. Data were recorded on adult emergence, postembryonic developmental period, number of mature eggs in the ovary, fecundity, larval survival from artificially implanted eggs; and the tannins, soluble sugars, and protein content of 10-day old and mature grains during the 1982-91 rainy and post-rainy seasons. Adult emergence was significantly lower in the midge-resistant genotypes compared with the susceptible controls. Initiation of adult emergence was delayed by 4–8 days on DJ 6514, IS 8571, IS 9807, IS 10712, IS 19474, IS 19512, ICSV 830 and ICSV 197. Postembryonic developmental period was prolonged on DJ 6514, IS 15107, IS 3461, IS 7005, IS 19474, ICSV 831 and ICSV 197. However, the delay in adult emergence or the extended developmental period was not observed during the post-rainy season in some genotypes. These differences in the expression of antibiosis to midge in resistant genotypes over seasons may be attributed to the effect of environmental conditions on the insect development and chemical composition of sorghum grain. Amounts of tannins and proteins were generally greater in the midge-resistant lines compared with the susceptible ones (except tannins in DJ 6514) while the soluble sugars were low in the midge-resistant lines (except TAM 2566). These differences in chemical composition of the grain between genotypes and variations over seasons have been discussed in relation to the expression of antibiosis mechanism of resistance to the sorghum midge. Antibiosis to sorghum midge was also evident in terms of smaller size of larvae, lower number of eggs in the ovary, reduced fecundity, and larval survival. Midge-resistant lines have diverse effects on the biology of this insect. Antibiosis along with other components of resistance can be used to develop cultivars with stable resistance to C. sorghicola.
Optimal protocols for sequence-based characterization of the human vaginal microbiome

The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment, but also to the use of conflicting methodologies to study its microbial composition. Here we systematically assess best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region has the best theoretical properties, but limitations of current sequencing technologies mean that the V3-V4 region performs equally well. Both of these approaches present very good agreement with qPCR quantification of key taxa, provided an appropriate bioinformatic pipeline is used. Shotgun metagenomic sequencing presents an interesting alternative to 16S amplification and sequencing, but it is not without its challenges. We have assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and – use, reference database of vaginal taxa. This strategy performed as well as the best performing previously published strategies. Despite the many advantages of shotgun sequencing none of the shotgun approaches assessed here had as good agreement with the qPCR data as 16S rRNA gene sequencing. Importance The vaginal microbiome has been connected to a wide range of health outcomes, from susceptibility to sexually transmitted infections to gynecological cancers and pregnancy outcomes. This has led to a thriving research environment, but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail for them to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.
Comparative evaluation of trace elements in the scalp hair of arthritis patients and healthy donors

This study was aimed to evaluate the comparative distribution, correlation and apportionment of selected elements (Ca, Cd, Co, Cr, Cu, Fe, Mg, Mn, Pb and Zn) in the scalp hair of arthritis patients and healthy subjects. The hair samples collected from the patients (rheumatoid and osteoarthritis) and healthy donors were digested in nitric acid and perchloric acid mixture, followed by the quantification of trace elements using atomic absorption spectrometry. In the case of healthy donors, highest mean concentration was shown by Ca (3240 µg g−1), followed by Mg (340 µg g−1), Zn (192 µg g−1), Fe (184 µg g−1) and Pb (27 µg g−1), whereas, the estimated average metal levels in rheumatoid arthritis and osteoarthritis patients were 3160, 290, 197, 61 and 23 µg g−1, and 3090, 300, 182, 50 and 21 µg g−1, respectively. Most of the elements revealed diverse and random distribution in the scalp hair of the donor groups. The correlation study pointed out significant disparities in the mutual relationships among the trace elements in the patients and controls. Principal component analysis and cluster analysis of the element data manifested diverse apportionment of the selected elements in the scalp hair of the patients compared with the healthy counterparts.
Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function

Terminal selectors are transcription factors (TFs) that establish during development and maintain throughout life post-mitotic neuronal identity. We previously showed that UNC-3/Ebf, the terminal selector of C. elegans cholinergic motor neurons (MNs), acts indirectly to prevent alternative neuronal identities (Feng et al., 2020). Here, we globally identify the direct targets of UNC-3. Unexpectedly, we find that the suite of UNC-3 targets in MNs is modified across different life stages, revealing “temporal modularity” in terminal selector function. In all larval and adult stages examined, UNC-3 is required for continuous expression of various protein classes (e.g., receptors, transporters) critical for MN function. However, only in late larvae and adults, UNC-3 is required to maintain expression of MN-specific TFs. Minimal disruption of UNC-3’s temporal modularity via genome engineering affects locomotion. Another C. elegans terminal selector (UNC-30/Pitx) also exhibits temporal modularity, supporting the potential generality of this mechanism for the control of neuronal identity.
Where in the leaf is intercellular CO2 (Ci)? Considerations and recommendations for assessing gaseous diffusion in leaves

The assumptions that water vapor exchange occurs exclusively through stomata, that the intercellular airspace is fully saturated with water vapor, and that CO2 gradients are negligible between stomata and the intercellular airspace have enabled significant advancements in photosynthetic gas exchange research for nearly 60 years via calculation of intercellular CO2 (Ci). However, available evidence suggests that these assumptions may be overused. Here we review the literature surrounding evidence for and against the assumptions made by Moss & Rawlins (1963). We reinterpret data from the literature by propagating different rates of cuticular water loss, CO2 gradients, and unsaturation through the data. We find that in general, when cuticle conductance is less than 1% of stomatal conductance, the assumption that water vapor exchange occurs exclusively through stomata has a marginal effect on gas exchange calculations, but this is not true when cuticle conductance exceeds 5% of stomatal conductance. Our analyses further suggest that CO2 and water vapor gradients have stronger impacts at higher stomatal conductance, while cuticle conductance has a greater impact at lower stomatal conductance. Therefore, we recommend directly measuring Ci whenever possible, measuring apoplastic water potentials to estimate humidity inside the leaf, and exercising caution when interpreting data under conditions of high temperature and/or low stomatal conductance, and when a species is known to have high cuticular conductance. Highlight Leaf water vapor and CO2 exchange have been successfully used to model photosynthetic biochemistry. We review critical assumptions in these models and make recommendations about which need to be re-assessed.
Promoter activity-based case-control association study on SLC6A4 highlighting hypermethylation and altered amygdala volume in male patients with schizophrenia

Associations between altered DNA methylation of the serotonin transporter (5-HTT)-encoding gene SLC6A4 and early life adversity, mood and anxiety disorders, and amygdala reactivity have been reported. However, few studies have examined epigenetic alterations of SLC6A4 in schizophrenia (SZ). We examined CpG sites of SLC6A4, whose DNA methylation levels have been reported to be altered in bipolar disorder, using three independent cohorts of patients with SZ and age-matched controls. We found significant hypermethylation of a CpG site in SLC6A4 in male patients with SZ in all three cohorts. We showed that chronic administration of risperidone did not affect the DNA methylation status at this CpG site using common marmosets, and that in vitro DNA methylation at this CpG site diminished the promoter activity of SLC6A4. We then genotyped the 5-HTT-linked polymorphic region (5-HTTLPR) and investigated the relationship among 5-HTTLPR, DNA methylation, and amygdala volume using brain imaging data. We found that patients harboring low-activity 5-HTTLPR alleles showed hypermethylation and they showed a negative correlation between DNA methylation levels and left amygdala volumes. These results suggest that hypermethylation of the CpG site in SLC6A4 is involved in the pathophysiology of SZ, especially in male patients harboring low-activity 5-HTTLPR alleles.
Baffling: A cheater strategy using self-made tools in tree crickets

Intense sexual selection in the form of mate choice can facilitate the evolution of different alternative reproductive strategies. These strategies can be condition-dependent, wherein genetically similar individuals express the strategy based on their condition. Our study shows that baffling, a mate attraction strategy using self-made acoustic amplifiers, employed by male tree crickets, is a classic example of a condition-dependent alternative strategy. We show that less preferred males, who are smaller or produce less loud calls, predominantly use this alternative strategy. Baffling allows these males to increase their call loudness and advertisement range, and attract a higher number of mates. Baffling also allows these males to deceive females into mating for longer durations with them. Our results suggest that the advantage of baffling in terms of sperm transfer is primarily limited to less preferred males, thus maintaining the polymorphism of calling strategies in the population. Impact statement This study shows that less preferred tree cricket males use an alternative signaling strategy to call louder, thus attracting and mating with otherwise choosy females using deception.
Determinants of Predictability in Multi-decadal Forest Community and Carbon Dynamics

Predictions from ecological models necessarily include five different uncertainties: demographic stochasticity, initial conditions, external forcing (i.e., drivers/covariates), parameters, and model processes. However, most predictions from process-based ecological models only account for a subset of these uncertainties (e.g. only demographic stochasticity). This underestimation of uncertainty runs the risk of producing precise, but inaccurate predictions. To address these limitations, we created a new generalizable ensemble state data assimilation algorithm that accommodates two common features of ecological data, zero-truncation and zero-inflation, and allows the estimation of process error and its covariance among multiple ecological variables. We then demonstrate the use of this novel algorithm by assimilating 50 years of tree-ring-estimated species-level biomass at Harvard Forest into a process-based forest gap model. Finally, we partitioned the variance in this hindcast to test long-standing assumptions in the ecological modeling community about which uncertainties dominate our ability to forecast forest community and carbon dynamics. Contrary to >40 years of research relying on stochastic forest gap models, we found that demographic stochasticity alone massively underestimated forecast uncertainty (0.09% of the total) and resulted in overconfident and biased model predictions. Similarly, despite decades of reliance on unconstrained spin-ups to initialize models, constraining initial conditions with data led to the largest increases in prediction accuracy. Counter to conventional wisdom from modeling other Earth system process, initial condition uncertainty declined very little over the forecast time period. Process variance, which heretofore had been difficult to estimate in mechanistic ecosystem model projections, dominated the prediction uncertainty over the forecast time period (49.1%), followed by meteorological uncertainty (32.5%). Parameter uncertainty, which has recently been the focus of the modeling community, contributed a modest 18.3%. These findings call into question much of our conventional wisdom about how to improve forest community and carbon cycle projections on multi-decadal to centennial time scales. This foundation can be used to test long-standing modeling assumptions across fields in global change biology and suggests a fairly significant reorientation of the modeling community toward better initialization of models with current observations and efforts to better quantify, propagate, and reduce process error. These approaches have the potential to improve both the accuracy of ecological forecasts and our understanding of the predictability of ecological processes.