Miracle-dz/UniFAR-FTUs huggingface dataset:
Contextual expectations shape cortical reinstatement of sensory representations

When making a turn at a familiar intersection, we know what items and landmarks will come into view. These perceptual expectations, or predictions, come from our knowledge of the context; however, it is unclear how memory and perceptual systems interact to support the prediction and reactivation of sensory details in cortex. To address this, human participants learned the spatial layout of animals positioned in a cross maze. During fMRI, participants of both sexes navigated between animals to reach a target, and in the process saw a predictable sequence of five animal images. Critically, to isolate activity patterns related to item predictions, rather than bottom-up inputs, one-fourth of trials ended early, with a blank screen presented instead. Using multivariate pattern similarity analysis, we reveal that activity patterns in early visual cortex, posterior medial regions, and the posterior hippocampus showed greater similarity when seeing the same item compared with different items. Further, item effects in posterior hippocampus were specific to the sequence context. Critically, activity patterns associated with seeing an item in visual cortex and posterior medial cortex, were also related to activity patterns when an item was expected, but omitted, suggesting sequence predictions were reinstated in these regions. Finally, multivariate connectivity showed that patterns in the posterior hippocampus at one position in the sequence were related to patterns in early visual cortex and posterior medial cortex at a later position. Together, our results support the idea that hippocampal representations facilitate sensory processing by modulating visual cortical activity in anticipation of expected items. SIGNIFICANCE STATEMENT Our visual world is a series of connected events, where we can predict what we might see next based on our recent past. Understanding the neural circuitry and mechanisms of the perceptual and memory systems that support these expectations is fundamental to revealing how we perceive and act in our world. Using brain imaging, we studied what happens when we expect to see specific visual items, and how such expectations relate to top-down memory signals. We find both visual and memory systems reflect item predictions, and moreover, we show that hippocampal activity supports predictions of future expected items. This demonstrates that the hippocampus acts to predict upcoming items, and reinstates such predictions in cortex.
Microtubule rescue at midzone edges promotes overlap stability and prevents spindle collapse during anaphase B

During anaphase B, molecular motors slide interpolar microtubules to elongate the mitotic spindle, contributing to the separation of chromosomes. However, sliding of antiparallel microtubules reduces their overlap, which may lead to spindle breakage, unless microtubules grow to compensate sliding. How sliding and growth are coordinated is still poorly understood. In this study, we have used the fission yeast S. pombe to measure microtubule dynamics during anaphase B. We report that the coordination of microtubule growth and sliding relies on promoting rescues at the midzone edges. This makes microtubules stable from pole to midzone, while their distal parts including the plus ends alternate between assembly and disassembly. Consequently, the midzone keeps a constant length throughout anaphase, enabling sustained sliding without the need for a precise regulation of microtubule growth speed. Additionally, we found that in S. pombe, which undergoes closed mitosis, microtubule growth speed decreases when the nuclear membrane wraps around the spindle midzone.
A Network-Centric Framework for the Evaluation of Mutual Exclusivity Tests on Cancer Drivers

One of the key concepts employed in cancer driver gene identification is that of mutual exclusivity (ME); a driver mutation is less likely to occur in case of an earlier mutation that has common functionality in the same molecular pathway. Several ME tests have been proposed recently, however the current protocols to evaluate ME tests have two main limitations. Firstly the evaluations are mostly with respect to simulated data and secondly the evaluation metrics lack a network-centric view. The latter is especially crucial as the notion of common functionality can be achieved through searching for interaction patterns in relevant networks. We propose a network-centric framework to evaluate the pairwise significances found by statistical ME tests. It has three main components. The first component consists of metrics employed in the network-centric ME evaluations. Such metrics are designed so that network knowledge and the reference set of known cancer genes are incorporated in ME evaluations under a careful definition of proper control groups. The other two components are designed as further mechanisms to avoid confounders inherent in ME detection on top of the network-centric view. To this end, our second objective is to dissect the side effects caused by mutation load artifacts where mutations driving tumor subtypes with low mutation load might be incorrectly diagnosed as mutually exclusive. Finally, as part of the third main component, the confounding issue stemming from the use of nonspecific interaction networks generated as combinations of interactions from different tissues is resolved through the creation and use of tissue-specific networks in the proposed framework. The data, the source code and useful scripts are available at: https://github.com/abu-compbio/NetCentric.
Fat specific adipose triglyceride lipase is necessary for iron-mediated lipolysis and lipid mobilization in response to negative energy balance

Maintenance of energy balance is essential for the overall health of an organism. In mammals, both negative and positive energy balance are associated with disease states. To maintain their energy balance within a defined homeostatic setpoint, mammals have evolved complex regulatory mechanisms that control energy intake and expenditure. Traditionally, studies have focused on understanding the role of macronutrient physiology in energy balance. In the present study, we examined the role of the essential micronutrient iron in regulating energy balance. Using a dietary model, we found that a short course of excess dietary iron caused a negative energy balance resulting in a severe whole body wasting phenotype. This disruption in energy balance was due to an iron dependent increase in energy expenditure caused by a heightened basal metabolic rate and activity level. Using a transgenic mouse model lacking adipose triglyceride lipase (ATGL) specifically in fat tissue, we found that to meet the increased energetic demands, dietary iron caused increased lipid utilization that required fat specific ATGL-mediated lipid mobilization and wasting of subcutaneous white adipose tissue deposits. When fed dietary iron, mice lacking fat-specific ATGL activity were protected from fat wasting, and developed a severe cachectic response that is necessary to meet the increased energetic demands caused by the dietary regimen. Our work highlights the multi-faceted role of iron regulation of organismal metabolism and provides a novel in vivo mechanism for micronutrient control of lipolysis that is necessary for regulating mammalian energy balance.
Translational modeling of non-traumatic raised intracranial pressure in rodents; the impact of diet-induced obesity on cephalic hypersensitivity and retinal degeneration

Elevated intracranial pressure (ICP) is a feature of critical cerebral disorders. Obesity has been linked to raised ICP, and especially to disorders such as idiopathic intracranial pressure (IIH). We aimed to explore the impact of diet-induced obesity (DIO) on ICP, cephalic sensitivity and structural retinal changes with the dual goal of developing a disease model for non-traumatic raised ICP and IIH. Rats were fed high-fat diet or matched control diet. To assess pain sensitivity, Von Frey and light/dark box testing were performed. Dual energy x-ray absorptiometry scanning was used to measure body composition. Optic nerve head and retinal structures were evaluated using optical coherence tomography. Intraocular pressure was assessed. Rats were then implanted with telemetric device for continuous ICP recording. At the end, eye histology and molecular analysis on choroid plexus (CP) and trigeminal ganglion (TG) were performed. The DIO rats had double the abdominal fat mass. ICP was 55% higher in obese rats (p=0.003). Altered pain thresholds were found in DIO rats as denoted by a lower periorbital threshold (p=0.0002). Expression of Calca and Trpv1 was elevated in TG. Furthermore, a peripapillary retinal nerve fiber layer swelling (p=0.0026) with subsequent neuroretinal degeneration p=0.02) was detected in DIO rats. There was a trend to increased expression of AQP1 and NKCC1 at CP. This study demonstrates for the first time that DIO leads to raised ICP, with clinically relevant sequalae. Our novel model for non-traumatic raised ICP could expand the knowledge regarding disorders with elevated ICP and IIH.
Evolution of andrenine bees reveals a long and complex history of faunal interchanges between the Americas during the Mesozoic and Cenozoic

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Among the main groups of bees, Andreninae sensu lato comprise about 3000 species widely distributed with greatest and disjunct diversity in arid areas of North America, South America, and the Palearctic region. Here, we present the first comprehensive dated phylogeny and historical biogeographic analysis for andrenine bees, including representatives of all currently recognized tribes. Our analyses rely on a dataset of 106 taxa and 7952 aligned nucleotide positions from one mitochondrial and six nuclear loci. Andreninae is strongly supported as a monophyletic group and the recovered phylogeny corroborates the commonly recognized clades for the group. Thus, we propose a revised tribal classification that is congruent with our phylogenetic results. The time-calibrated phylogeny and ancestral range reconstructions of Andreninae reveal a fascinating evolutionary history with Gondwana patterns that are unlike those observed in other subfamilies of bees. Andreninae arose in South America during the Late Cretaceous around 90 Million years ago (Ma) and the origin of tribes occurred through a relatively long time-window from this age to the Miocene. The early evolution of the main lineages took place in South America until the beginning of Paleocene with North American fauna origin from it and Palearctic from North America as results of multiple lineage interchanges between these areas by long-distance dispersal or hopping through landmass chains. Overall, our analyses provide strong evidence of amphitropical distributional pattern currently observed in Andreninae in the American continent as result at least three periods of possible land connections between the two American landmasses, much prior to the Panama Isthmus closure. The andrenine lineages reached the Palearctic region through four dispersal events from North America during the Eocene, late Oligocene and early Miocene, most probably via the Thulean Bridge. The few lineages with Afrotropical distribution likely originated from a Palearctic ancestral in the Miocene around 10 Ma when these regions were contiguous, and the Sahara Desert was mostly vegetated making feasible the passage by several organisms. Incursions of andrenine bees to North America and then onto the Old World are chronological congruent with distinct periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.
Is the genomics ‘cart’ before the restoration ecology ‘horse’? Insights from qualitative interviews and trends from the literature

Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation – a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives in harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasised the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems.
Sensing hand position in Ehlers-Danlos Syndrome

Purpose To explore the effect of joint hypermobility on acuity, and plasticity, of hand proprioception. Materials and Methods We compared proprioceptive acuity between EDS patients and controls. We then measured any changes in their estimate of hand position after participants adapted their reaches in response to altered visual feedback of their hand. The Beighton Scale was used to quantify the magnitude of joint hypermobility. Results There were no differences between the groups in the accuracy of estimates of hand location, nor in the visually-induced changes in hand location. However, EDS patients’ estimates were less precise when based purely on proprioception and could be partially predicted by Beighton score. Conclusions EDS patients are less precise at estimating their hand’s location when only afferent information is available, but the presence of efferent signalling may reduce this imprecision. Those who are more hypermobile are more likely to be imprecise.
Language in Behavioral Variant Frontotemporal Dementia: Another Stone to Be Turned in Latin America

Beyond canonical deficits in social cognition and interpersonal conduct, behavioral variant frontotemporal dementia (bvFTD) involves language difficulties in a substantial proportion of cases. However, since most evidence comes from high-income countries, the scope and relevance of language deficits in Latin American bvFTD samples remain poorly understood. As a first step toward reversing this scenario, we review studies reporting language measures in Latin American bvFTD cohorts relative to other groups. We identified 24 papers meeting systematic criteria, mainly targeting phonemic and semantic fluency, naming, semantic processing, and comprehension skills. The evidence shows widespread impairments in these domains, often related to overall cognitive disturbances. Some of these deficits may be as severe as in other diseases where they are more widely acknowledged, such as Alzheimer's disease. Considering the prevalence and informativeness of language deficits in bvFTD patients from other world regions, the need arises for more systematic research in Latin America, ideally spanning multiple domains, in diverse languages and dialects, with validated batteries. We outline key challenges and pathways of progress in this direction, laying the ground for a new regional research agenda on the disorder.
Association of Osteoarthritis With Changes in Structural Neuroimaging Markers Over Time Among Non-demented Older Adults

Objective: Although emerging evidence suggests that both osteoarthritis (OA) and brain atrophy (as assessed by structural neuroimaging markers) are associated with the risk of dementia, little is known about the association between OA and structural neuroimaging markers. This study aimed to examine the association of OA with changes in structural neuroimaging markers among non-demented older people. Methods: We examined the cross-sectional and longitudinal associations between OA and structural neuroimaging markers (hippocampal volume, entorhinal volume, ventricular volume, and volume of gray matter of the whole brain) among non-demented older people. We categorized our participants as those without OA (OA−) and those with OA (OA+). At baseline, we included 1,281 non-demented older adults, including 1,050 without OA and 231 with OA. Results: In the cross-sectional analysis, we did not observe any significant difference in structural neuroimaging markers between the two OA groups. In the longitudinal analysis, we found that compared to participants without OA, those with OA showed a steeper decline in volumes of the gray matter of the whole brain among non-demented older adults. Conclusions: OA was associated with a steeper decline in volumes of the gray matter of the whole brain over time among non-demented older people.
Genomic Copy Number Variants in CML Patients With the Philadelphia Chromosome (Ph+): An Update

Background Submicroscopic segmental imbalances detected by array-comparative genomic hybridization (array-CGH) were discovered to be common in chronic myeloid leukemia (CML) patients with t(9;22) as the sole chromosomal anomaly. To confirm the findings of the previous study and expand the investigation, additional CML patients with t(9;22) as the sole chromosomal anomaly were recruited and copy number variants (CNVs) were searched for. Methods Karyotyping tests were performed on 106 CML patients during January 2010–September 2019 in our Genetics Laboratory. Eighty-four (79.2%) patients had the Philadelphia (Ph) chromosome as the sole chromosomal anomaly. Only 49(58.3%) of these 84 patients had sufficient marrow or leukemia blood materials to additionally be included in the array-CGH analysis. Fluorescence in situ hybridization (FISH) was carried out to confirm the genes covered by the deleted or duplicated regions of the CNVs. Results 11(22.4%) out of the 49 patients were found to have one to three somatic segmental somatic segmental (CNVs), including fourteen deletions and three duplications. The common region associated with deletions was on 9q33.3-34.12. Identified in five (45.5%) of the 11 positive patients with segmental CNVs, the deletions ranged from 106 kb to 4.1 Mb in size. Two (18.2%) cases had a deletion in the ABL1-BCR fusion gene on der (9), while three (27.3%) cases had a deletion in the ASS1 gene. The remaining CNVs were randomly distributed on different autosomes. Conclusion Subtle genomic CNVs are relatively common in CML patients without cytogenetically visible additional chromosomal aberrations (ACAs). Long-term studies investigating the potential impact on patient prognosis and treatment outcome is underway.
From Farm to Fork: Crickets as Alternative Source of Protein, Minerals, and Vitamins

Globally, there is growing interest to integrate cricket-based ingredients (flour) into food products to combat food and nutrition insecurity. However, there is lack of information on in-depth nutrient profile of the two cricket species (Scapsipedus icipe and Gryllus bimaculatus), which are the most widely consumed in Africa. Here we determined the nutrient composition of two cricket species and compared them with published records of key animal and plant sources. Our results revealed that the crude protein contents of S. icipe and G. bimaculatus were similar (56.8 and 56.9%, respectively) and comparable to those of animal protein sources. Both cricket species had balanced amino acid profiles that are superior to that of animal and plant sources, except for histidine and cysteine. The protein digestibility of S. icipe and G. bimaculatus ranged between 80 and 88%, which is comparable to that of common plant foods but slightly lower than that of animal proteins. The iron, Zinc, and potassium contents were considerably higher in both cricket species compared to that of plant and animal sources. The calcium contents of both crickets (S. icipe and G. bimaculatus) was superior to that of plant and animal origin except for kidney beans and eggs, respectively. Riboflavin, thiamine, and folic acid concentrations of S. icipe and G. bimaculatus were superior to that of the conventional sources. Vitamin A levels were significantly higher in S. icipe compared to G. bimaculatus. This implies that S. icipe and G. bimaculatus can adequately contribute to our daily required nutrient intake. Thus, integrating cricket flours into ready-to-eat food products would address some of the most pressing nutritional deficiency challenges that many developing countries have to grapple with, particularly high risk to serious health problems such as anemia, poor pregnancy outcomes, hypertension, increased risk of morbidity and mortality, stunted growth and impaired physical and cognitive development. We conclude that edible crickets present unique opportunities for improving food and nutritional insecurity status of both resource-poor and Western populations.
Case Report: Paraneoplastic Hashimoto's Encephalopathy Associated With Lymphomatosis Cerebri With Periodic Synchronous Discharges Resembling Creutzfeldt–Jakob Disease

Hashimoto's encephalopathy (HE) is an autoimmune encephalopathy that presents with various clinical symptoms, including cognitive deterioration, convulsive seizures, and personality changes. HE is associated with thyroid autoimmunity; however, few cases have been reported to develop as paraneoplastic syndrome. Herein, we report the case of a 73-year-old woman with onset of rapidly progressive dementia. Brain magnetic resonance imaging showed diffuse T2 hyperintensity areas involving the bilateral cerebral white matter, right midbrain tegmental area, left cerebral peduncle, and right middle cerebellar peduncle without clear diffusion hyperintensities and gadolinium enhancement. Her neurological symptoms worsened rapidly, and she presented with the apallic syndrome. Electroencephalogram showed periodic synchronous discharge, suggestive of Creutzfeldt–Jakob disease. However, a brain biopsy revealed infiltration of atypical lymphoid cells expressing CD20, and the anti-NH2 terminal of the α-enolase antibody was detected, diagnosing the complication with lymphomatosis cerebri and HE. High-dose intravenous methylprednisolone therapy and oral prednisolone with whole cranial irradiation enabled her to have simple conversations and consume food orally; however, severe cognitive impairment persisted. Although HE is a rare complication of malignant lymphoma, clinicians should be aware that it could be strongly suspected if the clinical symptoms worsen in the absence of imaging changes.