Miracle-dz/UniFAR-FTUs huggingface dataset:
Modular‐level alterations of structure–function coupling in schizophrenia connectome

Convergent evidences have revealed that schizophrenia is associated with brain dysconnectivity, which leads to abnormal network organization. However, discrepancies were apparent between the structural connectivity (SC) and functional connectivity (FC) studies, and the relationship between structural and functional deficits in schizophrenia remains largely unknown. In this study, resting‐state functional magnetic resonance imaging and structural diffusion tensor imaging were performed in 20 patients with schizophrenia and 20 matched healthy volunteers (patients/controls = 19/17 after head motion rejection). Functional and structural brain networks were obtained for each participant. Graph theoretical approaches were employed to parcellate the FC networks into functional modules. The relationships between the entries of SC and FC were estimated within each module to identify group differences and their correlations with clinical symptoms. Although five common functional modules (including the default mode, occipital, subcortical, frontoparietal, and central modules) were identified in both groups, the patients showed a significantly reduced modularity in comparison with healthy participants. Furthermore, we found that schizophrenia‐related aberrations of SC–FC coupling exhibited complex patterns among modules. Compared with controls, patients showed an increased SC–FC coupling in the default mode and the central modules. Moreover, significant SC–FC decoupling was demonstrated in the occipital and the subcortical modules, which was associated with longer duration of illness and more severe clinical manifestations of schizophrenia. Taken together, these findings demonstrated that altered module‐dependent SC–FC coupling may underlie abnormal brain function and clinical symptoms observed in schizophrenia and highlighted the potential for using new multimodal neuroimaging biomarkers for diagnosis and severity evaluation of schizophrenia. Hum Brain Mapp 38:2008–2025, 2017. © 2017 Wiley Periodicals, Inc.
Response of Phytoplankton Photophysiology to Varying Environmental Conditions in the Sub-Antarctic and Polar Frontal Zone

Climate-driven changes are expected to alter the hydrography of the Sub-Antarctic Zone (SAZ) and Polar Frontal Zone (PFZ) south of Australia, in which distinct regional environments are believed to be responsible for the differences in phytoplankton biomass in these regions. Here, we report how the dynamic influences of light, iron and temperature, which are responsible for the photophysiological differences between phytoplankton in the SAZ and PFZ, contribute to the biomass differences in these regions. High effective photochemical efficiency of photosystem II (/ 0.4), maximum photosynthesis rate (), light-saturation intensity (), maximum rate of photosynthetic electron transport (1/), and low photoprotective pigment concentrations observed in the SAZ correspond to high chlorophyll and iron concentrations. In contrast, phytoplankton in the PFZ exhibits low / ( 0.2) and high concentrations of photoprotective pigments under low light environment. Strong negative relationships between iron, temperature, and photoprotective pigments demonstrate that cells were producing more photoprotective pigments under low temperature and iron conditions, and are responsible for the low biomass and low productivity measured in the PFZ. As warming and enhanced iron input is expected in this region, this could probably increase phytoplankton photosynthesis in this region. However, complex interactions between the biogeochemical processes (e.g. stratification caused by warming could prevent mixing of nutrients), which control phytoplankton biomass and productivity, remain uncertain.
Evaluating the Role of the EOF Analysis in 4DEnVar Methods

The four-dimensional variational data assimilation (4DVar) method is one of the most popular techniques used in numerical weather prediction. Nevertheless, the needs of the adjoint model and the linearization of the forecast model largely limit the wider applications of 4DVar. 4D ensemble-variational data assimilation methods (4DEnVars) exploit the strengths of the Ensemble Kalman Filter and 4DVar, and use the ensemble trajectories to directly estimate four-dimensional background error covariance. This study evaluates the role of the empirical orthogonal function (EOF) analysis in 4DEnVars. The widely-recognized 4DEnVar method DRP-4DVar (the Dimension-reduced projection 4DVar) is adopted as the representation of EOF analyses in this study. The performance of the Dimension-reduced projection 4DVar (DRP-4DVar), 4DEnVar (i.e., another traditional 4DEnVar scheme without EOF transformation), and the Ensemble Transform Kalman Filter (ETKF) was compared to demonstrate the effect of the EOF analysis in DRP-4DVar. Sensitivity experiments indicate that EOF analyses construct basis vectors in eigenvalue space and the dimension reduction in the DRP-4DVar approach helps improve computational efficiency and analysis accuracy. When compared with 4DEnVar and the ETKF, the DRP-4DVar demonstrates similar analysis root-mean-square error (RMSE) to 4DEnVar, whereas it surpasses the ETKF by 22.3%. In addition, sensitivity experiments of DRP-4DVar on the ensemble size, the assimilation window length, and the standard deviation of the initial perturbation imply that the DRP-4DVar with the optimized EOF truncation number is robust to a wide range of the parameters, but extremely low values should be avoided. The results presented here suggest the potential wide application of EOF analysis in the hybrid 4DEnVar methods.
Hardware-Based Workload Forensics and Malware Detection in Microprocessors

We investigate the possibility of performing workload forensics and/or malware detection in microprocessors through exclusively hardware-based methodologies. Specifically, we first introduce a general architecture which a hardware-based forensics or malware detection method would need to follow, as well as the various processor-level information which could potentially be harnessed to ensure system security and/or integrity. In contrast to traditional forensics and/or malware detection methods implemented at the operating system (OS) and/or the hypervisor level, whose data logging and monitoring systems are vulnerable to spoofing attacks at the same level, moving implementation to hardware ensures immunity to such attacks. This work focuses on two recent incarnations of this general concept, illustrating the effectiveness of hardware-based forensics and/or malware detection. Several other recent methods related to this topic are also discussed. Experimental results corroborate that even a low-cost hardware implementation can facilitate highly successful forensics analysis and/or malware detection, while taking advantage of its innate immunity to software-based attacks.
Diagnostic Value of the Reflux Disease Questionnaire in General Practice

Objectives: This study determined the diagnostic and therapeutic response of the Reflux Disease Questionnaire (RDQ) using the symptom association probability (SAP) as reference. In addition, the RDQ’s construct validity and its relationship to quality of life (QOL) were ascertained. Methods: Seventy-four patients with GORD symptoms (age 51 years (22–78); ♂62%) derived from primary care completed the RDQ, GSRS and QOLRAD before and after a 2 weeks’ course of esomeprazole 40 mg daily. The SAP was determined by a 24-hour pH recording before PPI treatment. The diagnostic abilities of the RDQ (total and 4 dimensions scores) were assessed with the area under the curve (AUC) of a receiver operating curve. RDQ scores before and after PPI treatment were compared with Wilcoxon tests. Multiple linear regressions assessed the RDQ’s construct validity (GSRS) and relationship to QOL (QOLRAD). Results: The AUCs were low for all RDQ dimensions (AUC <0.6). In the SAP-positive patients all RDQ dimensions improved (p < 0.0001) while the scores of the SAP negatives did not (heartburn p < 0.01; GORD and total score p < 0.05; regurgitation and dyspepsia n.s.). The RDQ was related to the total and reflux GSRS dimensions while the food and drink QOL dimension was linearly associated with the RDQ. Conclusions: The RDQ is a valid and reliable questionnaire with excellent construct validity and a good relationship to QOL. The diagnostic value of the RDQ in primary care is limited, but combination with an additional PPI treatment course might improve the RDQ’s ability to discriminate GORD patients according to their SAP outcome.
Effects of an NMDA antagonist on the auditory mismatch negativity response to transcranial direct current stimulation

Transcranial direct current stimulation (tDCS) is a non-invasive form of brain stimulation which uses a weak constant current to alter cortical excitability and activity temporarily. tDCS-induced increases in neuronal excitability and performance improvements have been observed following anodal stimulation of brain regions associated with visual and motor functions, but relatively little research has been conducted with respect to auditory processing. Recently, pilot study results indicate that anodal tDCS can increase auditory deviance detection, whereas cathodal tDCS decreases auditory processing, as measured by a brain-based event-related potential (ERP), mismatch negativity (MMN). As evidence has shown that tDCS lasting effects may be dependent on N-methyl-D-aspartate (NMDA) receptor activity, the current study investigated the use of dextromethorphan (DMO), an NMDA antagonist, to assess possible modulation of tDCS’s effects on both MMN and working memory performance. The study, conducted in 12 healthy volunteers, involved four laboratory test sessions within a randomised, placebo and sham-controlled crossover design that compared pre- and post-anodal tDCS over the auditory cortex (2 mA for 20 minutes to excite cortical activity temporarily and locally) and sham stimulation (i.e. device is turned off) during both DMO (50 mL) and placebo administration. Anodal tDCS increased MMN amplitudes with placebo administration. Significant increases were not seen with sham stimulation or with anodal stimulation during DMO administration. With sham stimulation (i.e. no stimulation), DMO decreased MMN amplitudes. Findings from this study contribute to the understanding of underlying neurobiological mechanisms mediating tDCS sensory and memory improvements.
Apollonian circle packings and closed horospheres on hyperbolic 3-manifolds

We obtain an asymptotic formula for the number of circles of curvature at most T in any given bounded Apollonian circle packing. For an integral packing, we obtain the upper bounds for the number of circles with prime curvature as well as of pairs of circles with prime curvatures, which are sharp up constant multiples. The main ingredient of our proof is the effective equidistribution of expanding horospheres on geometrically finite hyperbolic 3-manifolds under the assumption that the critical exponent of its fundamental group exceeds one.
A Bilinear Equalizer for Massive MIMO Systems

We present a novel approach for low-complexity equalizer design well suited for cellular massive MIMO systems. Our design allows to exploit the channel structure in terms of covariance matrices to improve the performance in the face of pilot-contamination, while basically keeping the complexity of a matched filter. This is achieved by restricting the equalizer to functions, which are bilinear in the received data signals and the observations from a training phase. The proposed design generalizes several previous approaches to equalizer design for massive MIMO. We show by asymptotic analysis that with the proposed design the achievable rate grows without bound for growing numbers of antennas even in the presence of pilot-contamination. We demonstrate with numerical results that the proposed design is competitive with more complex approaches in a practical cellular setup.
Impact of preoperative anemia on outcomes in patients undergoing curative resection for gastric cancer: a single‐institution retrospective analysis of 2163 Chinese patients

We sought to evaluate whether preoperative anemia was an important determinant of survival in gastric cancer (GC). A single institution cohort of 2163 GC patients who underwent curative resection were retrospectively analyzed. Anemia was defined as a preoperative hemoglobin level <120 g/L in males and <110 g/L in females. Overall survival (OS) was analyzed using the Kaplan–Meier method, and a multivariate Cox proportional hazards model was performed to identify the independent prognostic factor. Anemic patients had a poorer OS compared with nonanemic patients after resection for tumor–nodes–metastasis (TNM) stage III tumors (5‐year OS rate: 32.2% vs. 45.7%, P < 0.001) but not stage I (P = 0.480) or stage II (P = 0.917) tumors. Multivariate analysis revealed that preoperative anemia was an independent prognostic factor in TNM stage III (hazard ratio [HR], 1.771; 95% CI, 1.040–3.015; P = 0.035). In a stage‐stratified analysis, preoperative anemia was still independently associated with OS in TNM stages IIIa through IIIc (P < 0.001, P = 0.075, and P = 0.012, respectively), though the association was only marginal in stage IIIb. Of note, preoperative mild anemia had a similar prognostic value in TNM stage III GC. Furthermore, preoperative anemia was significantly associated with more perioperative transfusions, postoperative complications and several nutritional‐based indices, including the prognostic nutritional index (PNI), preoperative weight loss and performance status (all P < 0.05). Preoperative anemia, even mild anemia, was an important predictor of postoperative survival for TNM stage III GC.
Deletion of Slc26a1 and Slc26a7 Delays Enamel Mineralization in Mice

Amelogenesis features two major developmental stages—secretory and maturation. During maturation stage, hydroxyapatite deposition and matrix turnover require delicate pH regulatory mechanisms mediated by multiple ion transporters. Several members of the Slc26 gene family (Slc26a1, Slc26a3, Slc26a4, Slc26a6, and Slc26a7), which exhibit bicarbonate transport activities, have been suggested by previous studies to be involved in maturation-stage amelogenesis, especially the key process of pH regulation. However, details regarding the functional role of these genes in enamel formation are yet to be clarified, as none of the separate mutant animal lines demonstrates any discernible enamel defects. Continuing with our previous investigation of Slc26a1−/− and Slc26a7−/− animal models, we generated a double-mutant animal line with the absence of both Slc26a1 and Slc26a7. We showed in the present study that the double-mutant enamel density was significantly lower in the regions that represent late maturation-, maturation- and secretory-stage enamel development in wild-type mandibular incisors. However, the “maturation” and “secretory” enamel microstructures in double-mutant animals resembled those observed in wild-type secretory and/or pre-secretory stages. Elemental composition analysis revealed a lack of mineral deposition and an accumulation of carbon and chloride in double-mutant enamel. Deletion of Slc26a1 and Slc26a7 did not affect the stage-specific morphology of the enamel organ. Finally, compensatory expression of pH regulator genes and ion transporters was detected in maturation-stage enamel organs of double-mutant animals when compared to wild-type. Combined with the findings from our previous study, these data indicate the involvement of SLC26A1and SLC26A7 as key ion transporters in the pH regulatory network during enamel maturation.
An Optically Pumped Magnetometer Working in the Light-Shift Dispersed Mz Mode

We present an optically pumped magnetometer working in a new operational mode—the light-shift dispersed Mz (LSD-Mz) mode. It is realized combining various features; (1) high power off-resonant optical pumping; (2) Mz configuration, where pumping light and magnetic field of interest are oriented parallel to each other; (3) use of small alkali metal vapor cells of identical properties in integrated array structures, where two such cells are pumped by circularly polarized light of opposite helicity; and (4) subtraction of the Mz signals of these two cells. The LSD-Mz magnetometer’s performance depends on the inherent and very complex interplay of input parameters. In order to find the configuration of optimal magnetometer resolution, a sensitivity analysis of the input parameters by means of Latin Hypercube Sampling was carried out. The resulting datasets of the multi-dimensional parameter space exploration were assessed by a subsequent physically reasonable interpretation. Finally, the best shot-noise limited magnetic field resolution was determined within that parameter space. As the result, using two 50 mm3 integrated vapor cells a magnetic field resolution below 10 fT/√Hz at Earth’s magnetic field strength is possible.
Return to Work After Anatomic Total Shoulder Arthroplasty for Patients 55 Years and Younger at Average 5-Year Follow-up.

As the number of anatomic total shoulder arthroplasties performed on younger patients continues to grow, return to work after surgery becomes increasingly important. The purpose of this study was to evaluate the ability of anatomic total shoulder arthroplasty to return patients 55 years or younger to work postoperatively. A retrospective review was performed of consecutive anatomic total shoulder arthroplasty patients. Inclusion criteria were age 55 years or younger at surgery, greater than 2 years of follow-up, and employment within 3 years of surgery. Employment was stratified by intensity of work (sedentary, light, moderate, or heavy). Return to work status and time out of work were also evaluated. Fifty-two patients worked before surgery. Average age was 48.4 years, with average follow-up of 5.4 years. Seventy-three percent were male, and average body mass index was 28.0 kg/m2. Average visual analog scale score improved from 5.5 to 0.9 (P<.0001) and American Shoulder and Elbow Society score improved from 39.9 to 88.3 (P<.0001). Forty-eight (92%) of 52 returned to work postoperatively after an average of 2.1 months. When stratified by intensity, all patients with sedentary, light, or moderate work returned, whereas 64% returned to heavy work (P<.01). Eighty-seven percent were satisfied to very satisfied after surgery. In summary, most patients (92%) who undergo anatomic total shoulder arthroplasty at 55 years or younger return to work, on average, 2.1 months after surgery. [Orthopedics. 2018; 41(3):e310-e315. ].
A model of anterior cruciate ligament injury in cynomolgus monkeys developed via arthroscopic surgery

The anterior cruciate ligament (ACL) is an important structure that maintains the stability of knee joints. Animal models of ACL injury are helpful to explore its underlying mechanisms, and strategies for prevention, treatment and rehabilitation. Therefore, the aim of the present study was to develop an efficient model of ACL injury in cynomolgus monkeys via arthroscopic techniques. In the present study, 18 cynomolgus monkeys were randomly divided into a model group (n=6), a sham operation group (n=6) and a blank control group (n=6). One-quarter of the ACL was removed under arthroscopy in the model group. In the sham operation group, only arthroscopic exploration was performed as a control. In the blank control group, monkeys were housed under the same conditions for the same length of time. Magnetic resonance imaging examination was performed pre- and post-operatively, as well as measurements of the circumference of the thigh and calf, and of the maximum flexion degree of the knee. Anterior drawer test, Lachman test and pivot-shift tests were also performed. The results revealed that the injured side of the knees in the model group became unstable, as determined from evaluation of the physical tests. In conclusion, based on these findings, the modeling method of ACL injury was effective, and may contribute to the associated research concerning ACL injury.
P16 overexpression in BRAF-mutated gastrointestinal stromal tumors

ABSTRACT Background: The aims of this study were to analyze the histopathology, immunophenotype, molecular features, and prognosis in cases of BRAF-mutated gastrointestinal stromal tumors (GISTs) and to examine the p16 expression in these tumors, and further discuss its effects on tumor formation and progression. Methods: In all, 283 GIST cases (201 KIT mutants, 12 PDGFRA mutants and 70 wild-type) from the 2010 to 2014 surgical pathology files of the Department of Pathology at Nanjing Jinling Hospital were analyzed for mutations in BRAF exon 15. Patient follow-up and clinical data were collected if available in the medical records. To determine the clinicopathological features and potential molecular mechanism, the authors examined 10 BRAF-mutated GIST cases for KIT, DOG1, SMA, desmin, S-100, Ki-67 and p16 expression. Results: The authors identified 10 cases (3.5%) of BRAF (V600E) mutations in a series of 283 primary GISTs, without KIT (exons 9, 11, 13, 17) or PDGFRA (exons 12, 18) gene mutations. All 10 cases exhibited spindle-cell features, and the morphology and immunophenotype of these cases were no different from those in cases of KIT-mutated GISTs. The clinical results indicated that BRAF-mutated GISTs tended to occur more frequently in females (7/10), older individuals (mean age, 54.9 years) and the stomach (7/10), and that these tumors were low risk and exhibited low recurrence and mortality rates. Two different forms of p16 were identified, which presented with simultaneously strong and diffuse nuclear and cytoplasmic expression patterns. Conclusion: GISTs with the BRAF V600E mutation are relatively benign tumors with a distinctive molecular mechanism. The expression of the nuclear and cytoplasmic forms of p16 represent two independent mechanisms, and both seemed to control proliferation in response to oncogenic stimuli, protecting the cell from malignant transformation in BRAF-mutated GISTs.
Spectral Library Based Analysis of Arginine Phosphorylations in Staphylococcus aureus*

Reversible protein phosphorylation is one of the major mechanisms in the regulation of protein expression and protein activity, controlling physiological functions of the important human pathogen Staphylococcus aureus. Phosphorylations at serine, threonine and tyrosine are known to influence for example protein activity in central metabolic pathways and the more energy-rich phosphorylations at histidine, aspartate or cysteine can be found as part of two component system sensor domains or mediating bacterial virulence. In addition to these well-known phosphorylations, the phosphorylation at arginine residues plays an essential role. Hence, the deletion mutant S. aureus COL ΔptpB (protein tyrosine phosphatase B) was studied because the protein PtpB is assumed to be an arginine phosphatase. A gel-free approach was applied to analyze the changes in the phosphoproteome of the deletion mutant ΔptpB and the wild type in growing cells, thereby focusing on the occurrence of phosphorylation on arginine residues. In order to enhance the reliability of identified phosphorylation sites at arginine residues, a subset of arginine phosphorylated peptides was chemically synthesized. Combined spectral libraries based on phosphoenriched samples, synthetic arginine phosphorylated peptides and classical proteome samples provide a sophisticated tool for the analysis of arginine phosphorylations. This way, 212 proteins phosphorylated on serine, threonine, tyrosine or arginine residues were identified within the mutant ΔptpB and 102 in wild type samples. Among them, 207 arginine phosphosites were identified exclusively within the mutant ΔptpB, widely distributed along the whole bacterial metabolism. This identification of putative targets of PtpB allows further investigation of the physiological relevance of arginine phosphorylations and provides the basis for reliable quantification of arginine phosphorylations in bacteria.