Miracle-dz/UniFAR-FTUs huggingface dataset:
Cultural Attachment: From Behavior to Computational Neuroscience

Cultural attachment (CA) refers to processes that allow culture and its symbols to provide psychological security when facing threat. Epistemologically, whereas we currently have an adequate predictivist model of CA, it is necessary to prepare for a mechanistic approach that will not only predict, but also explain CA phenomena. Toward that direction, we here first examine the concepts and mechanisms that are the building blocks of both the prototypical maternal attachment as well as CA. Based on existing robust neuroscience models we associate these concepts and mechanisms with bona fide neurobiological functions to advance an integrative neurobiological model of CA. We further discuss the unresolved relationship of CA to other similar socio-cognitive concepts such as familiarity. Overall aim of the paper is to highlight the importance of integrating CA theory to computational approaches to culture and evolution (such as predictive processing computations explaining niche construction), as this will allow a dynamic interpretation of cultural processes.
Develop Your Case! How Controversial Cases, Subcases, and Moderated Cases Can Guide You Through Mixed Methods Data Analysis

In this article, we present mixed methods data analysis in educational research as a process of case development. We define a case as a theoretical construct that is developed through iterative and spiraling cycles of interaction between ideas and evidence. On a larger scale, cases develop over a period of several years or even decades, involving many studies. But cases also develop within a much smaller timescale, within studies. Development of cases within mixed methods studies is the theme of this article. We define the purpose for any mixed methods study as to acquire detailed insight into the case, subcases, and the way the subcases are moderated. Developing a case starts with identifying a phenomenon that will be the object of research. A phenomenon can be investigated empirically once researchers are able to identify specific contexts, localized in time and space, in which the phenomenon occurs. At that point, an underdeveloped case has come into being, and the specific contexts in which the case occurs are called instantiations of the case. Connected to each case are claims, statements about the case that are used to describe the case more precisely and to distinguish cases from non-cases. Developing these claims is the aim of the analysis processes. Case development includes three different research processes—namely, resolving a controversial case, developing subcases, and developing a moderated case. Case development typically occurs in this order; however, each of these processes can but do not need to be present. When cases develop, they typically become controversial for some time. Some research studies support a specific claim, while other research studies refute this claim. Next to claims that apply to all instantiations of a case, claims may be developed that apply to only some of the case’s instantiations. In that case, claims are used to distinguish subcases. A moderated case is developed when researchers come to understand under which circumstances their claim does and does not apply, which leads to their subcases. This is called “moderation” of their claim.
GS-CA Compounds: First-In-Class HIV-1 Capsid Inhibitors Covering Multiple Grounds

Recently reported HIV-1 capsid (CA) inhibitors GS-CA1 and GS-6207 (an analog of GS-CA1) are first-in-class compounds with long-acting potential. Reportedly, both compounds have greater potency than currently approved anti-HIV drugs. Due to the limited access to experimental data and the compounds themselves, a detailed mechanism of their inhibition is yet to be delineated. Using crystal structures of capsid-hexamers bound to well-studied capsid inhibitor PF74 and molecular modeling, we predict that GS-CA compounds bind in the pocket that is shared by previously reported CA inhibitors and host factors. Additionally, comparative modeling suggests that GS-CA compounds have unique structural features contributing to interactions with capsid. To test their proposed binding mode, we also report the design of a cyclic peptide combining structural units from GS-CA compounds, host factors, and previously reported capsid inhibitors. This peptide (Pep-1) binds CA-hexamer with a docking score comparable to GS-CA compounds. Affinity determination by MicroScale thermophoresis (MST) assays showed that CA binds Pep-1 with a ~7-fold better affinity than well-studied capsid inhibitor PF74, suggesting that it can be developed as a possible CA inhibitor.
Semiparametric Estimation of Task-Based Dynamic Functional Connectivity on the Population Level

Dynamic functional connectivity (dFC) estimates time-dependent associations between pairs of brain region time series as typically acquired during functional MRI. dFC changes are most commonly quantified by pairwise correlation coefficients between the time series within a sliding window. Here, we applied a recently developed bootstrap-based technique (Kudela et al., 2017) to robustly estimate subject-level dFC and its confidence intervals in a task-based fMRI study (24 subjects who tasted their most frequently consumed beer and Gatorade as an appetitive control). We then combined information across subjects and scans utilizing semiparametric mixed models to obtain a group-level dFC estimate for each pair of brain regions, flavor, and the difference between flavors. The proposed approach relies on the estimated group-level dFC accounting for complex correlation structures of the fMRI data, multiple repeated observations per subject, experimental design, and subject-specific variability. It also provides condition-specific dFC and confidence intervals for the whole brain at the group level. As a summary dFC metric, we used the proportion of time when the estimated associations were either significantly positive or negative. For both flavors, our fully-data driven approach yielded regional associations that reflected known, biologically meaningful brain organization as shown in prior work, as well as closely resembled resting state networks (RSNs). Specifically, beer flavor-potentiated associations were detected between several reward-related regions, including the right ventral striatum (VST), lateral orbitofrontal cortex, and ventral anterior insular cortex (vAIC). The enhancement of right VST-vAIC association by a taste of beer independently validated the main activation-based finding (Oberlin et al., 2016). Most notably, our novel dFC methodology uncovered numerous associations undetected by the traditional static FC analysis. The data-driven, novel dFC methodology presented here can be used for a wide range of task-based fMRI designs to estimate the dFC at multiple levels—group-, individual-, and task-specific, utilizing a combination of well-established statistical methods.
Duration of Humoral and Cellular Immunity 8 Years After Administration of Reduced Doses of the 17DD-Yellow Fever Vaccine

The present study aims to determine whether 17DD-YF-specific humoral and cellular immunological memory is maintained 8-years after primary vaccination with subdoses (10,447IU;3,013IU;587IU;158IU;31IU). For this purpose, this follow-up study was carried out in a subset of volunteers (n = 98) originally enrolled in the dose-response study in 2009 and 46 non-vaccinated controls. Our results demonstrated that vaccinees, who had seroconverted following primary vaccination and had not been revaccinated, present similar neutralizing antibodies levels and YF-specific cellular memory, particularly CMCD4 and EMCD8 as compared to the reference full dose (27,476IU). Although, PRNT seropositivity rates were similar across subgroups (94, 82, 83, 94, 80, and 91%, correspondingly), only doses above 587IU elicited similar iterative proportion of seropositivity rates, calculated as a progressive decrease on seropositivity rates along time (89, 80, 80, and 91%, respectively) as compared to 158IU and 31IU (68 and 46%, respectively). Noteworthy were the strong positive correlations (“EMCD4,EMCD8” and “TNFCD8,IFNCD8”) observed in most subdoses, except for 31IU. Major similarities underscored the preserved antibody titers and the outstanding levels of EMCD8, relevant correlates of protection for YF-specific immunity. These findings provide evidences to support the regular use of dose sparing strategy for YF vaccine in adults.
Interleukin-17 Promotes Migration and Invasion of Human Cancer Cells Through Upregulation of MTA1 Expression

Interleukin-17 (IL-17) has been shown to promote development of prostate, colon, skin, lung, breast, and pancreatic cancer. The purpose of this study was to determine if IL-17 regulates MTA1 expression and its biological consequences. Human cervical cancer HeLa and human prostate cancer DU-145 cell lines were used to test if IL-17 regulates metastasis associated 1 (MTA1) mRNA and protein expression using quantitative reverse transcription-polymerase chain reaction and Western blot analysis, respectively. Cell migration and invasion were studied using wound healing assays and invasion chamber assays. Thirty-four human cervical tissues were stained for IL-17 and MTA1 using immunohistochemical staining. We found that IL-17 increased MTA1 mRNA and protein expression in both cell lines. Cell migration was accelerated by IL-17, which was abolished by knockdown of MTA1 expression with small interference RNA (siRNA). Further, cell invasion was enhanced by IL-17, which was eliminated by MTA1 knockdown. Human cervical intra-epithelial neoplasia (CIN) and cervical cancer tissues had increased number of IL-17-positive cells and MTA1 expression compared to normal cervical tissues. The number of IL-17-positive cells was positively correlated with MTA1 expression. These findings demonstrate that IL-17 upregulates MTA1 mRNA and protein expression to promote HeLa and DU-145 cell migration and invasion.
Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.
The Role of Prefrontal Cortical Surface Area and Volume in Preclinical Suicidal Ideation in a Non-Clinical Sample

Suicidal ideation (SUI) can occur in the absence of concomitant psychiatric diagnoses, and even normal levels can be problematic among individuals experiencing excess stress or lack of social support. The objective of this study was to investigate the neuroanatomical basis of SUI in non-clinical human populations who are within the normal limits of SUI, after accounting for elevated stress and perceived lack of social support. Neuroanatomical data were collected from 55 healthy individuals (mean age 30.9 ± 8.1 years, 27 females) whose depression severity levels were below the Diagnostic and Statistical Manual of Mental Disorders criteria. Measures of SUI, aggression, stress, non-support, and treatment rejection were collected from the treatment-consideration scales (TCS) of the Personality Assessment Inventory (PAI). Correlations between standardized SUI scores and three brain morphometry measures, including vertex wise cortical thickness (CT), cortical surface area (CSA), and cortical volume (CV), were estimated for each participant, controlling for age, sex, intracranial volume, and the remaining TCS measures. We observed a significant negative association between scores on SUI and both CSA and CV (cluster-forming threshold of p < 0.005, clusterwise threshold of p < 0.05, FDR corrected for multiple comparisons) within the left rostral middle frontal gyrus. Our findings suggest that greater CSA and CV within the dorsolateral prefrontal cortex are associated with reduced SUI in a non-clinical population with mild levels of stress and perceived lack of social support. Because the dorsolateral prefrontal cortex has been broadly linked to cognitive reappraisal, self-critical thoughts, and emotional regulation, greater CSA and CV within these regions may lead to better mental health by protecting healthy individuals from engaging in SUI during periods of stress and perceived insufficient social support. As our data consisted of only healthy individuals with non-clinical levels of SUI, further investigation will be necessary to explore the neural basis of SUI in populations who may be at greater risk of future suicidal behavior
Alzheimer Disease Pathogenesis: Insights From Molecular and Cellular Biology Studies of Oligomeric Aβ and Tau Species

Alzheimer disease (AD) represents an oncoming epidemic that without an effective treatment promises to exact extraordinary human and financial burdens. Studies of pathogenesis are essential for defining targets for discovering disease-modifying treatments. Past studies of AD neuropathology provided valuable, albeit limited, insights. Nevertheless, building on these findings, recent studies have provided an increasingly rich harvest of genetic, molecular and cellular data that are creating unprecedented opportunities to both understand and treat AD. Among the most significant are those documenting the presence within the AD brain of toxic oligomeric species of Aβ and tau. Existing data support the view that such species can propagate and spread within neural circuits. To place these findings in context we first review the genetics and neuropathology of AD, including AD in Down syndrome (AD-DS). We detail studies that support the existence of toxic oligomeric species while noting the significant unanswered questions concerning their precise structures, the means by which they spread and undergo amplification and how they induce neuronal dysfunction and degeneration. We conclude by offering a speculative synthesis for how oligomers of Aβ and tau initiate and drive pathogenesis. While 100 years after Alzheimer’s first report there is much still to learn about pathogenesis and the discovery of disease-modifying treatments, the application of new concepts and sophisticated new tools are poised to deliver important advances for combatting AD.
Danggui Buxue Tang, a Chinese Herbal Decoction Containing Astragali Radix and Angelicae Sinensis Radix, Modulates Mitochondrial Bioenergetics in Cultured Cardiomyoblasts

Danggui Buxue Tang (DBT) is an ancient herbal mixture containing Astragali Radix and Angelicae Sinensis Radix, and which are commonly consumed for “qi-invigorating” (i.e., stimulating vital energy/energy metabolism) as traditional Chinese medicine (TCM). The pharmacological activities of DBT in anti-oxidation, estrogenic, hematopoietic, and immunogenic have been reported; however, the role of DBT in cellular energy metabolism has not been determined. Here, we employed an extracellular flux analyzer to evaluate the mitochondrial respiration of cultured H9C2 cardiomyoblasts in present of DBT. The herbal extract of DBT was qualified chemically for the major ingredients, i.e. astragaloside, calycosin, formononetin, Z-ligustilide, and ferulic acid. The anti-oxidant activities of DBT, as well as its major ingredients, were determined by Folin-Ciocalteu assay, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay, and protective effect in tert-butyl hydroperoxide (tBHP)-treated cultured cardiomyoblasts. In addition, a real-time oxygen consumption rate (OCR) in herbal extract-treated cultured cardiomyoblasts was revealed by using a Seahorse extracellular flux analyzer. In addition, the transcript expressions of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PCG-1α) and other genes relating to mitochondria biogenesis were determined in cardiomyoblasts under different herbal treatments. DBT possessed the strongest anti-oxidant activity and protective effects on the oxidatively stressed cardiomyoblasts. By revealing the OCR in mitochondria, the health state of cultured cardiomyoblasts under DBT was improved via increase of basal respiration, proton leak, non-mitochondria, and adenosine triphosphate (ATP) production. Furthermore, the transcriptional activities of genes responsible for mitochondrial biogenesis and DNA replication were stimulated by application of DBT in cultures.
Substitution of Human Papillomavirus Type 16 L2 Neutralizing Epitopes Into L1 Surface Loops: The Effect on Virus-Like Particle Assembly and Immunogenicity

Cervical cancer caused by infection with human papillomaviruses (HPVs) is the fourth most common cancer in women globally, with the burden mainly in developing countries due to limited healthcare resources. Current vaccines based on virus-like particles (VLPs) assembled from recombinant expression of the immunodominant L1 protein are highly effective in the prevention of cervical infection; however, these vaccines are expensive and type-specific. Therefore, there is a need for more broadly protective and affordable vaccines. The HPV-16 L2 peptide sequences 108-120, 65-81, 56-81, and 17-36 are highly conserved across several HPV types and have been shown to elicit cross-neutralizing antibodies. To increase L2 immunogenicity, L1:L2 chimeric VLPs (cVLP) vaccine candidates were developed. The four L2 peptides mentioned above were substituted into the DE loop of HPV-16 L1 at position 131 (SAC) or in the C-terminal region at position 431 (SAE) to generate HPV-16-derived L1:L2 chimeras. All eight chimeras were transiently expressed in Nicotiana benthamiana via Agrobacterium tumefaciens-mediated DNA transfer. SAC chimeras predominantly assembled into higher order structures (T = 1 and T = 7 VLPs), whereas SAE chimeras assembled into capsomeres or formed aggregates. Four SAC and one SAE chimeras were used in vaccination studies in mice, and their ability to generate cross-neutralizing antibodies was analyzed in HPV pseudovirion-based neutralization assays. Of the seven heterologous HPVs tested, cross-neutralization with antisera specific to chimeras was observed for HPV-11 (SAE 65-18), HPV-18 (SAC 108-120, SAC 65-81, SAC 56-81, SAE 65-81), and HPV-58 (SAC 108-120). Interestingly, only anti-SAE 65-81 antiserum showed neutralization of homologous HPV-16, suggesting that the position of the L2 epitope display is critical for maintaining L1-specific neutralizing epitopes.
Promoting Self-Regulatory Management of Chronic Pain Through Dohsa-hou: Single-Case Series of Low-Functioning Hemodialysis Patients

Hemodialysis patients suffer from long-term pain that drains their energy and contributes to behavioral interference and other negative effects on their daily lives that result in or exacerbate functional limitations. In addition, they deal with dietary restrictions, symptoms such as itching, lack of energy, and psychological stressors like the loss of self-concept and self-esteem. Self-regulation involves the capacity to notice, inform, and modulate responses and behavior, and research indicates that it promotes rehabilitation in chronic pain patients. Research on the aspects of self-regulation afforded by the Japanese psychotherapy Dohsa-hou correspond to psychological processes tied to the sense of self-control that clients realize over their body movements. This study pilot tested a hospital-integrated implementation of Dohsa-hou relaxation tasks as a chronic pain management behavioral intervention for five female hemodialysis patients between the ages of 59–62 years. We conducted an ABABABA single-case design to compare baseline A-phases (treatment-as-usual: TAU) taken at recurring 1 week intervals (three sessions per week for a total of 4 weeks, 12 total recordings) with an intervention of Dohsa-hou B-phases every 4 weeks (three sessions per week for 12 weeks, 36 total recordings) over the span of 4 months to compare effectiveness. Visual Analogue Scale (VAS) pain scores between phases were taken and self-regulatory progress was tracked and summarized from a series of semi-structured interviews. Visual analysis of scores for each participant as single cases indicated decreases for the Dohsa-hou phase compared to baseline treatment-as-usual. As a result, participants reported using Dohsa-hou to reduce pain and experienced improvements in quality of life associated with greater self-regulatory capacity to attend to personal care and domestic activities. These preliminary findings suggest that Dohsa-hou body movement relaxation tasks were feasible as a coping skill in a hospital-integrated setting and at home and show promise for promoting quality of life vis-a-vis the management of severe and chronic bodily pain associated with end-stage renal disease and its treatment, particularly by improving aspects of pain-mediated self-regulatory fatigue.
Sepsis: Inflammation Is a Necessary Evil

Sepsis is one of the leading causes of deaths world-wide and yet there are no therapies available other than ICU treatment. The patient outcome is determined by a complex interplay between the pro and anti-inflammatory responses of the body i.e., a homeostatic balance between these two competing events to be achieved for the patient’s recovery. The initial attempts on drug development mainly focused on controlling inflammation, however, without any tangible outcome. This was despite most deaths occurring during the immune paralysis stage of this biphasic disease. Recently, the focus has been shifting to understand immune paralysis (caused by apoptosis and by anti-inflammatory cytokines) to develop therapeutic drugs. In this review we put forth an argument for a proper understanding of the molecular basis of inflammation as well as apoptosis for developing an effective therapy.