A survey of experimental stimulus presentation code sharing in major areas of psychology.

Computer code plays a vital role in modern science, from the conception and design of experiments through to final data analyses. Open sharing of code has been widely discussed as being advantageous to the scientific process, allowing experiments to be more easily replicated, helping with error detection, and reducing wasted effort and resources. In the case of psychology, the code used to present stimuli is a fundamental component of many experiments. It is not known, however, the degree to which researchers are sharing this type of code. To estimate this, we conducted a survey of 400 psychology papers published between 2016 and 2021, identifying those working with the open-source tools Psychtoolbox and PsychoPy that openly share stimulus presentation code. For those that did, we established if it would run following download and also appraised the code's usability in terms of style and documentation. It was found that only 8.4% of papers shared stimulus code, compared to 17.9% sharing analysis code and 31.7% sharing data. Of shared code, 70% ran directly or after minor corrections. For code that did not run, the main error was missing dependencies (66.7%). The usability of the code was moderate, with low levels of code annotation and minimal documentation provided. These results suggest that stimulus presentation code sharing lags behind other forms of code and data sharing, potentially due to less emphasis on such code in open-science discussions and in journal policies. The results also highlight a need for improved documentation to maximize code utility.

Targeting the histone demethylase PHF8-mediated PKCα-Src-PTEN axis in HER2-negative gastric cancer.

Targeted treatments for advanced gastric cancer (GC) are needed, particularly for HER2-negative GC, which represents the majority of cases (80 to 88%). In this study, in silico analyses of the lysine histone demethylases (KDMs) involved in diverse biological processes and diseases revealed that PHD finger protein 8 (PHF8, KDM7B) was significantly associated with poor clinical outcome in HER2-negative GC. The depletion of PHF8 significantly reduced cancer progression in GC cells and in mouse xenografts. PHF8 regulated genes involved in cell migration/motility based on a microarray analysis. Of note, PHF8 interacted with c-Jun on the promoter of PRKCA which encodes PKCα. The depletion of PHF8 or PKCα greatly up-regulated PTEN expression, which could be rescued by ectopic expression of a PKCα expression vector or an active Src. These suggest that PTEN destabilization occurs mainly via the PKCα-Src axis. GC cells treated with midostaurin or bosutinib significantly suppressed migration in vitro and in zebrafish models. Immunohistochemical analyses of PHF8, PKCα, and PTEN showed a positive correlation between PHF8 and PKCα but negative correlations between PHF8 and PTEN and between PKCα and PTEN. Moreover, high PHF8-PKCα expression was significantly correlated with worse prognosis. Together, our results suggest that the PKCα-Src-PTEN pathway regulated by PHF8/c-Jun is a potential prognostic/therapeutic target in HER2-negative advanced GC.

Two RNA subunits and POT1a are components of Arabidopsis telomerase.

Telomerase is a ribonucleoprotein (RNP) reverse transcriptase whose essential RNA subunit (TER) functions as a template for telomere repeat synthesis. Here we report the identification of two divergent TER moieties in the flowering plant Arabidopsis thaliana. Although both TER1 and TER2 copurify with telomerase activity and serve as templates for telomerase in vitro, depletion of TER1, but not TER2, leads to decreased telomerase activity and progressive telomere shortening in vivo. Moreover, mutation of the templating domain in TER1 results in the incorporation of mutant telomere repeats on chromosome ends. Thus, TER1 provides the major template for telomerase in vivo. We also show that POT1a binds TER1 with a Kd of 2 × 10(-7) M and the two components assemble into an enzymatically active RNP in vivo. In contrast, TER1-POT1b and TER2-POT1a associations were not observed. In other organisms POT1 proteins bind telomeric DNA and provide chromosome end protection. We propose that duplication of TER and POT1 in Arabidopsis fueled the evolution of novel protein-nucleic acid interactions and the migration of POT1 from the telomere to the telomerase RNP.

IgG, IgM, and IgA antinuclear antibodies in discoid and systemic lupus erythematosus patients.

IgG antinuclear antibodies (ANAs) are elevated in patients with systemic lupus erythematosus (SLE) compared with patients with discoid lupus erythematosus (DLE). To provide an expanded immunologic view of circulating ANAs in lupus patients, we compared the expressions of IgG, IgM, and IgA ANAs in DLE and SLE patients. In this cross-sectional study, sera from age-, gender-, and ethnic-matched SLE (N = 35), DLE (N = 23), and normal patients (N = 22) were tested for IgG, IgM, and IgA ANAs using enzyme-linked immunosorbent assays (ELISAs) and indirect immunofluorescence (IIF) with monkey esophagus as substrate. ELISAs showed elevated levels of IgG ANA, IgM ANA, and IgG/IgM ANA ratios in SLE patients compared with DLE and normal patients. IgA ANA expression was higher in SLE and DLE patients versus normal patients. IIF studies showed higher percentages of patients positive for IgG, IgM, and IgA ANAs in the SLE group. Higher IgG/IgM ANA ratios in SLE than DLE show enhanced class-switching and a more sustained humoral response in SLE. They also suggest a potential connection of IgM ANAs with disease containment.

Epidemiology of orthopedic fractures and other injuries among inpatients admitted due to traffic accidents: a 10-year nationwide survey in Taiwan.

To investigate the major injury patterns associated with traffic accidents and evaluate the risk factors of the main injury, a survey of Taiwan's national insurance admission data between 2002 and 2011 was performed. The incidence of traffic-accidents-related hospitalization was between 9.17% and 11.54% and the average mortality rate of the inpatients admitted due to traffic accidents was 0.68%. Of all inpatients due to road traffic accidents in Taiwan, orthopedic fractures were the most common injuries that accounted for 29.36% of them. There were a total of 391,197 cases of three orthopedic fracture groups that were divided into (1) fracture of upper limb, (2) fracture of lower limb, and (3) fracture of spine and trunk. An increase in national medical cost used for inpatients with orthopedic fractures was noted and ranged from US$ 45.6 million to US$ 86 million annually. These orthopedic fracture patterns were frequently associated with other injuries especially head injuries (ranged from 14% to 26%). A significant relation to male gender, older age, low income, and admission to high-level hospital to the observed fracture patterns was observed.

DBCP: a web server for disulfide bonding connectivity pattern prediction without the prior knowledge of the bonding state of cysteines.

The proper prediction of the location of disulfide bridges is efficient in helping to solve the protein folding problem. Most of the previous works on the prediction of disulfide connectivity pattern use the prior knowledge of the bonding state of cysteines. The DBCP web server provides prediction of disulfide bonding connectivity pattern without the prior knowledge of the bonding state of cysteines. The method used in this server improves the accuracy of disulfide connectivity pattern prediction (Q(p)) over the previous studies reported in the literature. This DBCP server can be accessed at http://120.107.8.16/dbcp or http://140.120.14.136/dbcp.

Alpha-Mangostin Reduces Pericellular Fibronectin on Suspended Tumor Cells and Therapeutically, but Not Prophylactically, Suppresses Distant Metastasis.

Major cancer deaths can be ascribed to distant metastasis to which the assembly of pericellular fibronectin (periFN) on suspended tumor cells (STCs) in the bloodstream that facilitate endothelial attachment can lead. Even though mangosteen pericarps (MP) extracts and the major component α-mangostin (α-MG) exhibit potent cancer chemopreventive properties, whether they can prophylactically and therapeutically be used as dietary nutraceuticals to prevent distant metastasis by suppressing periFN assembly on STCs within the circulation remains obscure. Immunofluorescence staining, MTT assays, flow cytometric assays, immunoblotting, and experimental metastasis mouse models were used to detect the effects of MP extracts or α-MG on periFN on STCs, tumor cell proliferation and apoptosis, the AKT activity, and tumor lung metastasis. The periFN assembly on STCs was significantly diminished upon treatments of STCs with either α-MG or MP extracts in a dose-dependent manner without inhibiting cell proliferation and viability due to increased AKT activity. Pretreatment of STCs with α-MG appeared to suppress tumor lung metastasis and prolong mouse survival rates. Oral gavage with MP extracts could therapeutically, but not prophylactically, prevent lung metastasis of STCs. We concluded that MP extracts or the major component α-MG may therapeutically serve as a potent anti-metastatic nutraceutical.

Modulating inhibitory control with direct current stimulation of the superior medial frontal cortex.

The executive control of voluntary action involves not only choosing from a range of possible actions but also the inhibition of responses as circumstances demand. Recent studies have demonstrated that many clinical populations, such as people with attention-deficit hyperactivity disorder, exhibit difficulties in inhibitory control. One prefrontal area that has been particularly associated with inhibitory control is the pre-supplementary motor area (Pre-SMA). Here we applied non-invasive transcranial direct current stimulation (tDCS) over Pre-SMA to test its role in this behavior. tDCS allows for current to be applied in two directions to selectively excite or suppress the neural activity of Pre-SMA. Our results showed that anodal tDCS improved efficiency of inhibitory control. Conversely, cathodal tDCS showed a tendency towards impaired inhibitory control. To our knowledge, this is the first demonstration of non-invasive intervention tDCS altering subjects' inhibitory control. These results further our understanding of the neural bases of inhibitory control and suggest a possible therapeutic intervention method for clinical populations.

Revisiting the effects of transcranial direct current stimulation on pattern-reversal visual evoked potentials.

Despite increasing growth of interest in transcranial direct current stimulation (tDCS), its underlying mechanisms are still unclear. With many claims based on the anodal-excitation and cathodal-inhibition dichotomy originally observed in the motor cortex, surprisingly few studies have examined these fundamental polarity-specific effects beyond the motor cortex. The after-effects of tDCS on the visual cortex are of particular interest because of their potential application to vision restoration and migraine treatment. Yet the limited studies revealed conflicting results. Here we investigated whether polarity-specific tDCS effects exist in the visual cortex. In a counterbalanced within-subject crossover design, 20 healthy subjects each completed three sessions of anodal, cathodal and sham tDCS (2 mA for 20 min) applied over the visual cortex. Pattern-reversal visual evoked potentials (VEP) and their habituation slopes were measured at five time-points immediately before, after and every 15 min following the end of tDCS. Compared to sham, we found no significant tDCS induced after-effects on VEP amplitudes or habituation slopes, supported by strong evidence from Bayesian statistics. Neither were there any after-effects of tDCS on EEG power of the frequency of stimulus presentation, theta or alpha band. In conclusion, our results challenge previous findings of robust polarity-dependent after-effects of tDCS over the visual cortex.

Targeting KDM4B that coactivates c-Myc-regulated metabolism to suppress tumor growth in castration-resistant prostate cancer.

Rationale: The progression of prostate cancer (PCa) to castration-resistant PCa (CRPC) despite continuous androgen deprivation therapy is a major clinical challenge. Over 90% of patients with CRPC exhibit sustained androgen receptor (AR) signaling. KDM4B that removes the repressive mark H3K9me3/2 is a transcriptional activator of AR and has been implicated in the development of CRPC. However, the mechanisms of KDM4B involvement in CRPC remain largely unknown. Here, we sought to demonstrate the molecular pathway mediated by KDM4B in CRPC and to provide proof-of-concept evidence that KDM4B is a potential CRPC target. Methods: CRPC cells (C4-2B or CWR22Rv1) depleted with KDM4B followed by cell proliferation (in vitro and xenograft), microarray, qRT-PCR, Seahorse Flux, and metabolomic analyses were employed to identify the expression and metabolic profiles mediated by KDM4B. Immunoprecipitation was used to determine the KDM4B-c-Myc interaction region. Reporter activity assay and ChIP analysis were used to characterize the KDM4B-c-Myc complex-mediated mechanistic actions. The clinical relevance between KDM4B and c-Myc was determined using UCSC Xena analysis and immunohistochemistry. Results: We showed that KDM4B knockdown impaired CRPC proliferation, switched Warburg to OXPHOS metabolism, and suppressed gene expressions including those targeted by c-Myc. We further demonstrated that KDM4B physically interacted with c-Myc and they were co-recruited to the c-Myc-binding sequence on the promoters of metabolic genes (LDHA, ENO1, and PFK). Importantly, KDM4B and c-Myc synergistically promoted the transactivation of the LDHA promoter in a demethylase-dependent manner. We also provided evidence that KDM4B and c-Myc are co-expressed in PCa tissue and that high expression of both is associated with worse clinical outcome. Conclusions: KDM4B partners with c-Myc and serves as a coactivator of c-Myc to directly enhance c-Myc-mediated metabolism, hence promoting CRPC progression. Targeting KDM4B is thus an alternative therapeutic strategy for advanced prostate cancers driven by c-Myc and AR.

The distribution of cultivable oral anaerobic microbiota identified by MALDI-TOF MS in healthy subjects and in patients with periodontal disease.

In this study, we aimed to identify the cultivatable oral anaerobic bacterial distribution in oral cavity by MALDI-TOF Biotyper. The bacterial distribution of three groups, including subjects with/without periodontal disease, two clusters of age (60 years as the cutoff), and before/after treatment, were investigated in this study. There were 38 participants recruited in this study, involving 18 subjects with moderate to severe periodontal-infected patients and 20 healthy controls. Total number of 126 bacterial species were identified by MALDI-TOF MS. The relative abundance of Streptococcus gordonii and Streptococcus intermedius in periodontal patients is higher than healthy controls indicating potential biomarkers for periodontal disease. Participants with periodontal disease were subdivided in to two clusters of age (60 years as the cutoff), 11 and 7 participants were age <60 years and>60 years, respectively. Meanwhile, the incidence of Streptococcus pneumoniae and Streptococcus oralis infection were higher in the subjects above 60 years old than below. Moreover, the bacterial distribution between pre-treatment and post-treatment was similar indicating that basic treatment without the ability to redistribute the microbiota. In summary, the cultivable oral anaerobic bacteria were identified by MALDI-TOF MS and the bacterial distribution shifting was shown to be associated with the progress of periodontal disease to aging and basic treatment. This study provided information for diagnosis and treatment guidelines for oral healthcare.

Prognostic Significance of O-GlcNAc and PKM2 in Hormone Receptor-Positive and HER2-Nonenriched Breast Cancer.

Predictive metabolic biomarkers for the recurrent luminal breast cancer (BC) with hormone receptor (HR)-positive and human epidermal growth factor receptor type 2 (HER2)-negative are lacking. High levels of O-GlcNAcylation (O-GlcNAc) and pyruvate kinase isoenzyme M2 (PKM2) are associated with malignancy in BC; however, the association with the recurrence risk remains unclear. We first conduct survival analysis by using the METABRIC dataset to assess the correlation of PKM2 expression with BC clinical outcomes. Next, patients with HR+/HER2- luminal BC were recruited for PKM2/O-GlcNAc testing. Logistic regression and receiver operating characteristic curve analysis were performed to evaluate the 10-year DFS predicted outcome. Survival analysis of the METABRIC dataset revealed that high expression of PKM2 was significantly associated with worse overall survival in luminal BC. The high expression of O-GlcNAc or PKM2 was a significant independent marker for poor 10-year DFS using immunohistochemical analysis. The PKM2 or O-GlcNAc status was a significant predictor of DFS, with the combination of PKM2-O-GlcNAc status and T stage greatly enhancing the predictive outcome potential. In summary, O-GlcNAc, PKM2, and T stage serve as good prognostic discriminators in HR+/HER2- luminal BC.

Human ribonuclease 1 serves as a secretory ligand of ephrin A4 receptor and induces breast tumor initiation.

Human ribonuclease 1 (hRNase 1) is critical to extracellular RNA clearance and innate immunity to achieve homeostasis and host defense; however, whether it plays a role in cancer remains elusive. Here, we demonstrate that hRNase 1, independently of its ribonucleolytic activity, enriches the stem-like cell population and enhances the tumor-initiating ability of breast cancer cells. Specifically, secretory hRNase 1 binds to and activates the tyrosine kinase receptor ephrin A4 (EphA4) signaling to promote breast tumor initiation in an autocrine/paracrine manner, which is distinct from the classical EphA4-ephrin juxtacrine signaling through contact-dependent cell-cell communication. In addition, analysis of human breast tumor tissue microarrays reveals a positive correlation between hRNase 1, EphA4 activation, and stem cell marker CD133. Notably, high hRNase 1 level in plasma samples is positively associated with EphA4 activation in tumor tissues from breast cancer patients, highlighting the pathological relevance of the hRNase 1-EphA4 axis in breast cancer. The discovery of hRNase 1 as a secretory ligand of EphA4 that enhances breast cancer stemness suggests a potential treatment strategy by inactivating the hRNase 1-EphA4 axis.

NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants.

The sequential deletion method is generally used to locate the functional domain of a protein. With this method, in order to find the various N-terminal truncated mutants, researchers have to investigate the ATG-like codons, to design various multiplex polymerase chain reaction (PCR) forward primers and to do several PCR experiments. This web server (N-terminal Truncated Mutants Generator for cDNA) will automatically generate groups of forward PCR primers and the corresponding reverse PCR primers that can be used in a single batch of a multiplex PCR experiment to extract the various N-terminal truncated mutants. This saves much time and money for those who use the sequential deletion method in their research. This server is available at http://oblab.cs.nchu.edu.tw:8080/WebSDL/.

Noninvasive measurement of glucose concentration on human fingertip by optical coherence tomography.

A method is proposed for determining the glucose concentration on the human fingertip by extracting two optical parameters, namely the optical rotation angle and the depolarization index, using a Mueller optical coherence tomography technique and a genetic algorithm. The feasibility of the proposed method is demonstrated by measuring the optical rotation angle and depolarization index of aqueous glucose solutions with low and high scattering, respectively. It is shown that for both solutions, the optical rotation angle and depolarization index vary approximately linearly with the glucose concentration. As a result, the ability of the proposed method to obtain the glucose concentration by means of just two optical parameters is confirmed. The practical applicability of the proposed technique is demonstrated by measuring the optical rotation angle and depolarization index on the human fingertip of healthy volunteers under various glucose conditions.

Symmetrical peripheral gangrene in sepsis after treatment with inotropes.

Symmetrical peripheral gangrene (SPG) is characterized by sudden onset of peripheral, frequently symmetrical, gangrene in the absence of major vascular occlusive disease. We report a case of four limb SPG caused by septic shock with disseminated intravascular coagulation (DIC) that had been treated with inotropes. This case shows that SPG may be present as a complication of sepsis due to systematic derangement that affects a wide range of organ systems, including coagulation and microcirculation. Early recognition and prompt management of sepsis and optimization of the process of weaning off the inotropes at the earliest opportunity are necessary to avoid SPG.

A subset of CD163+ macrophages displays mixed polarizations in discoid lupus skin.

INTRODUCTION: Lesional skin of patients with discoid lupus erythematosus (DLE) contains macrophages, whose polarization has yet to be investigated. To test our hypothesis that M1 macrophages would be increased in DLE skin, we examined transcriptome alterations in immune cell gene expression and macrophage features in DLE and normal skin by using gene expression and histochemical approaches. METHODS: Gene expression of RNA from DLE lesional and normal control skin was compared by microarrays and quantitative real-time polymerase chain reaction (RT-PCR). Both skin groups were analyzed for CD163 expression by immunohistochemistry. Double immunofluorescence studies were performed to characterize protein expression of CD163+ macrophages. RESULTS: DLE skin had twice as many upregulated genes than downregulated genes compared with normal skin. Gene set enrichment analysis comparing differentially expressed genes in DLE and normal skin with previously published gene sets associated with M1 and M2 macrophages showed strong overlap between upregulated genes in DLE skin and M1 macrophages. Quantitative RT-PCR showed that several M1 macrophage-associated genes--e.g., chemokine (C-X-C motif) ligand 10 (CXCL10), chemokine (C-C motif) ligand 5 (CCL5), and signal transducer and activator of transcription 1 (STAT1)-had amplified mRNA levels in DLE skin. CD163+ macrophages were increased near the epidermal-dermal junction and perivascular areas in DLE skin compared with normal skin. However, double immunofluorescence studies of CD163+ macrophages revealed minor co-expression of M1 (CXCL10, tumor necrosis factor-alpha, and CD127) and M2 (CD209 and transforming growth factor-beta) macrophage-related proteins in DLE skin. CONCLUSION: Whereas a subset of CD163+ macrophages displays mixed polarizations in DLE skin, other immune cells such as T cells can contribute to the expression of these macrophage-related genes.

Differential expression of BAFF and its receptors in discoid lupus erythematosus patients.

BACKGROUND: B-cell activating factor of the TNF family (BAFF) promotes the maturation and survival of B cells. Because BAFF levels are elevated in systemic lupus erythematosus (SLE) patients, BAFF has been the target of emerging therapies for SLE, such as belimumab. Levels of BAFF and its receptors in discoid lupus erythematosus (DLE) patients are unknown. OBJECTIVE: To compare skin and blood mRNA and protein levels of BAFF and its receptors BAFF-R, TACI, and BCMA in DLE subjects with (DLE+/SLE+ (N=28)) and without SLE (DLE+/SLE- (N=35)), psoriasis subjects (N=11), and normal subjects (N=42). METHODS: We used quantitative real-time PCR to measure blood and skin BAFF, BAFF-R, TACI, and BCMA mRNA, sandwich ELISAs to measure sera BAFF, and immunohistochemistry to evaluate BAFF and BAFF-R skin protein expression. RESULTS: BAFF mRNA and protein levels were highest in DLE+/SLE+blood, followed by DLE+/SLE-, psoriasis, and normal blood. BAFF protein also correlated with anti-nuclear antibodies, and autoantibodies against double-stranded DNA, single-stranded DNA, and ribonucleoprotein, and Systemic Lupus Erythematosus Disease Activity Index scores in DLE patients. While showing no difference between DLE+/SLE+ and DLE+/SLE- skin, BAFF and its receptors mRNA were up-regulated in DLE skin vs. normal and psoriasis skin. DLE skin had higher percentages of BAFF-R⁺ inflammatory cells, likely T cells and macrophages, than psoriasis and normal skin. CONCLUSIONS: BAFF may be a serologic marker of systemic disease in DLE patients. BAFF and its receptors are elevated in DLE skin, suggesting that targeted therapies against these proteins could treat refractory DLE patients.

The role of superior temporal sulcus in the control of irrelevant emotional face processing: A transcranial direct current stimulation study.

Emotional faces are often salient cues of threats or other important contexts, and may therefore have a large effect on cognitive processes of the visual environment. Indeed, many behavioral studies have demonstrated that emotional information can modulate visual attention and eye movements. The aim of the present study was to investigate (1) how irrelevant emotional face distractors affect saccadic behaviors and (2) whether such emotional effects reflect a specific neural mechanism or merely biased selective attention. We combined a visual search paradigm that incorporated manipulation of different types of distractor (fearful faces or scrambled faces) and delivered anodal transcranial direct current stimulation (tDCS) over the superior temporal sulcus and the frontal eye field to investigate the functional roles of these areas in processing facial expressions and eye movements. Our behavioral data suggest that irrelevant emotional distractors can modulate saccadic behaviors. The tDCS results showed that while rFEF played a more general role in controlling saccadic behavior, rSTS is mainly involved in facial expression processing. Furthermore, rSTS played a critical role in processing facial expressions even when such expressions were not relevant to the task goal, implying that facial expressions and processing may be automatic irrespective of the task goal.