Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of anhedonia and suicidal ideation in patients with treatment-refractory depression after intravenous ketamine infusions

Abstract Objectives Accumulating evidence suggests that the effects of ketamine administered intravenously at subanaesthetic doses on both anhedonic symptoms and suicidal ideation occur independently of depressive symptoms in major depressive disorder (MDD) and bipolar disorder (BD). This study sought to determine the relationship between anhedonia and suicidal ideation after serial ketamine infusions. Methods A total of 79 subjects with either treatment-refractory MDD (n = 60) or BD (n = 19) were included in a clinical ketamine study. The Montgomery–Åsberg Depression Rating Scale (MADRS) anhedonia factor and the first five items of the Scale for Suicidal Ideations (SSI-Part I) were used to assess anhedonia symptoms and suicidal ideation, respectively. Results At baseline, anhedonia, as measured by the MADRS, was not significantly associated with suicidal ideation or specific suicide-related ideation as measured by SSI-Part I (all p’s > 0.05). Only the ‘wish to die’ and ‘desire to make a suicide attempt’ items were positively associated with anhedonia at two weeks after the sixth ketamine infusion, which was independent of the reductions in depressive symptoms (all p’s < 0.05). Conclusion Anhedonia as measured by the MADRS appeared to not be positively related to suicidal ideation after serial ketamine infusions. KEY POINTS Serial ketamine (0.5 mg/kg) infusions have shown quick and dramatic antisuicidal and antianhedonic effects in patients with depression. The association between anhedonia and suicidal ideation after serial ketamine infusions is unclear. Anhedonia appeared to not be positively related to suicidal ideation after serial ketamine infusions.
Immune Checkpoint Inhibitors and Tuberculosis Infection in Lung Cancer: A Case Series and Systematic Review With Pooled Analysis

The association between immune checkpoint inhibitors (ICIs) and tuberculosis (TB) infection in patients with lung cancer remains largely elusive. We performed a systematic review and conducted a retrospective analysis of TB infection in patients with lung cancer and ICI exposure to assess the clinical characteristics and outcomes using PubMed, EMBASE, and the Cochrane Library. The time interval from ICI administration to diagnosis of TB between patients with and without a history of TB was compared using Kaplan–Meier analysis. A multivariate Cox regression model was used to identify potential risk factors associated with the time interval of TB development. Twenty‐four studies including 53 patients with lung cancer were included. The median age of the patients was 64 years. Eight patients had a history of TB. The median time interval from ICI administration to TB diagnosis was 3 months. In retrospective analysis, 5 (1.16%, 95%CI 0.38% to 2.68%) patients with lung cancer developed TB during ICI treatment. The median time interval was 10.4 months. In a pooled analysis, the median time interval in the without‐TB and with‐TB groups was 7.00 and 2.35 months, respectively (P = .034). Multivariate Cox regression analyses revealed a history of TB to be an independent factor affecting the time interval of TB activation in patients with lung cancer and ICI exposure (HR 3.59; 95%CI 1.17 to 11.02; P = .026). Therefore, TB infection should be considered in patients with lung cancer during or after ICI treatment. Moreover, we found TB history to be a positive risk factor for a shorter median time interval from ICI to TB diagnosis in patients with lung cancer receiving ICI.
Color Classification of Extrasolar Giant Planets: Prospects and Cautions

Atmospheric characterization of directly imaged planets has thus far been limited to ground-based observations of young, self-luminous, Jovian planets. Near-term space- and ground- based facilities like WFIRST and ELTs will be able to directly image mature Jovian planets in reflected light, a critical step in support of future facilities that aim to directly image terrestrial planets in reflected light (e.g., HabEx, LUVOIR). These future facilities are considering the use of photometry to classify planets. Here, we investigate the intricacies of using colors to classify gas-giant planets by analyzing a grid of 9120 theoretical reflected light spectra spread across different metallicities, pressure–temperature profiles, cloud properties, and phase angles. We determine how correlated these planet parameters are with the colors in the WFIRST photometric bins and other photometric bins proposed in the literature. Then we outline under what conditions giant planet populations can be classified using several supervised multivariate classification algorithms. We find that giant planets imaged in reflected light can be classified by metallicity with an accuracy of >90% if they are a prior known to not have significant cloud coverage in the visible part of the atmosphere, and at least three filter observations are available. If the presence of clouds is not known a priori, directly imaged planets can be more accurately classified by their cloud properties, as oppposed to metallicity or temperature. Furthermore, we are able to distinguish between cloudy and cloud-free populations with >90% accuracy with three filter observations. Our statistical pipeline is available on GitHub and can be extended to optimize science yield of future mission concepts.
Deterministic and stochastic behaviour of non-Brownian spheres in sheared suspensions

The dynamics of macroscopically homogeneous sheared suspensions of neutrally buoyant, non-Brownian spheres is investigated in the limit of vanishingly small Reynolds numbers using Stokesian dynamics. We show that the complex dynamics of sheared suspensions can be characterized as a chaotic motion in phase space and determine the dependence of the largest Lyapunov exponent on the volume fraction ϕ. We also offer evidence that the chaotic motion is responsible for the loss of memory in the evolution of the system and demonstrate this loss of correlation in phase space. The loss of memory at the microscopic level of individual particles is also shown in terms of the autocorrelation functions for the two transverse velocity components. Moreover, a negative correlation in the transverse particle velocities is seen to exist at the lower concentrations, an effect which we explain on the basis of the dynamics of two isolated spheres undergoing simple shear. In addition, we calculate the probability distribution function of the transverse velocity fluctuations and observe, with increasing ϕ, a transition from exponential to Gaussian distributions. The simulations include a non-hydrodynamic repulsive interaction between the spheres which qualitatively models the effects of surface roughness and other irreversible effects, such as residual Brownian displacements, that become particularly important whenever pairs of spheres are nearly touching. We investigate, for very dilute suspensions, the effects of such a non-hydrodynamic interparticle force on the scaling of the particle tracer diffusion coefficients Dy and Dz, respectively, along and normal to the plane of shear, and show that, when this force is very short-ranged, both are proportional to ϕ2 as ϕ → 0. In contrast, when the range of the non-hydrodynamic interaction is increased, we observe a crossover in the dependence of Dy on ϕ, from ϕ2 to ϕ as ϕ → 0. We also estimate that a similar crossover exists for Dz but at a value of ϕ one order of magnitude lower than that which we were able to reach in our simulations.
Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation

Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
Block-induced Complex Structures Building the Flare-productive Solar Active Region 12673

Solar active region (AR) 12673 produced 4 X-class, 27 M-class, and numerous lower-class flares during its passage across the visible solar disk in 2017 September. Our study is to answer the questions why this AR was so flare-productive and how the X9.3 flare, the largest one of the past decade, took place. We find that there was a sunspot in the initial several days, and then two bipolar regions emerged nearby it successively. Due to the standing of the pre-existing sunspot, the movement of the bipoles was blocked, while the pre-existing sunspot maintained its quasi-circular shaped umbra only with the disappearance of a part of penumbra. Thus, the bipolar patches were significantly distorted, and the opposite polarities formed two semi-circular shaped structures. After that, two sequences of new bipolar regions emerged within the narrow semi-circular zone, and the bipolar patches separated along the curved channel. The new bipoles sheared and interacted with the previous ones, forming a complex topological system, during which numerous flares occurred. At the highly sheared region, a great deal of free energy was accumulated. On September 6, one negative patch near the polarity inversion line began to rapidly rotate and shear with the surrounding positive fields, and consequently the X9.3 flare erupted. Our results reveal that the block-induced complex structures built the flare-productive AR and the X9.3 flare was triggered by an erupting filament due to the kink instability. To better illustrate this process, a block-induced eruption model is proposed for the first time.
The Discovery of Rapid X-Ray Oscillations in the Tail of the SGR 1806–20 Hyperflare

We have discovered rapid quasi-periodic oscillations (QPOs) in RXTE/PCA measurements of the pulsating tail of the 2004 December 27 giant flare of SGR 1806-20. QPOs at ~92.5 Hz are detected in a 50 s interval starting 170 s after the onset of the giant flare. These QPOs appear to be associated with increased emission by a relatively hard unpulsed component and are seen only over phases of the 7.56 s spin period pulsations away from the main peak. QPOs at ~18 and ~30 Hz are also detected ~200-300 s after the onset of the giant flare. This is the first time that QPOs are unambiguously detected in the flux of a soft gamma-ray repeater or any other magnetar candidate. We interpret the highest QPOs in terms of the coupling of toroidal seismic modes with Alfvén waves propagating along magnetospheric field lines. The lowest frequency QPO might instead provide indirect evidence on the strength of the internal magnetic field of the magnetar.
Obtaining sparse distributions in 2D inverse problems Journal of Magnetic Resonance

The mathematics of inverse problems has relevance across numerous estimation problems in science and engineering. L 1 regularization has attracted recent attention in reconstructing the system properties in the case of sparse inverse problems; i.e., when the true property sought is not adequately described by a continuous distribution, in particular in Compressed Sensing image reconstruction. In this work, we focus on the application of L 1 regularization to a class of inverse problems; relaxation-relaxation, T 1 – T 2 , and diffusion-relaxation, D – T 2 , correlation experiments in NMR, which have found widespread applications in a number of areas including probing surface interactions in catalysis and characterizing ﬂuid composition and pore structures in rocks. We introduce a robust algorithm for solving the L 1 regular- ization problem and provide a guide to implementing it, including the choice of the amount of regularization used and the assignment of error estimates. We then show experimentally that L 1 regularization has signiﬁcant advantages over both the Non-Negative Least Squares (NNLS) algorithm and Tikhonov regularization. It is shown that the L 1 regularization algorithm stably recovers a distribution at a signal to noise ratio < 20 and that it resolves relaxation time constants and diffusion coefﬁcients differing by as little as 10%. The enhanced resolving capability is used to measure the inter and intra particle concentrations of a mixture of hexane and dodecane present within porous silica beads immersed within a bulk liquid phase; neither NNLS nor Tikhonov regularization are able to provide this resolution. This experimental study shows that the approach enables discrimination between different chemical species when direct spectroscopic discrimination is impossible, and hence measurement of chemical composition within por- ous media, such as catalysts or rocks, is possible while still being stable to high
Robust quantum state transfer via topological edge states in superconducting qubit chains

Robust quantum state transfer (QST) is an indispensable ingredient in scalable quantum information processing. Here we present an experimentally feasible mechanism for realizing robust QST via topologically protected edge states in superconducting qubit chains. Using superconducting Xmon qubits with tunable couplings, we construct generalized Su-Schrieffer-Heeger models and analytically derive the wave functions of topological edge states. We find that such edge states can be employed as a quantum channel to realize robust QST between remote qubits. With a numerical simulation, we show that both single-qubit states and two-qubit entangled states can be robustly transferred in the presence of sizable imperfections in the qubit couplings. The transfer fidelity demonstrates a wide plateau at the value of unity in the imperfection magnitude. This approach is general and can be implemented in a variety of quantum computing platforms.
Effects of chitin and chitosan on root growth, biochemical defense response and exudate proteome of Cannabis sativa

Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. No significant effects on plant defense were observed upon chitin treatment. These results indicate that colloidal chitosan significantly promoted production and secretion of plant defense proteins in C. sativa root system and could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases. Highlight Chitosan induces defense protein productions and secretions in the root tissues and exudates of C. sativa, offering a potential pathway to enhance plant resistance against fungal attack.
Discovery of prevalent, clinically actionable tumor neoepitopes via integrated biochemical and cell-based platforms

Strategies for maximizing the potency and specificity of cancer immunotherapies have sparked efforts to identify recurrent epitopes presented in the context of defined tumor-associated neoantigens. Discovering these “neoepitopes” can be difficult owing to the limited number of peptides that arise from a single point mutation, a low number of copies presented on the cell surface, and variable binding specificity of the human leukocyte antigen (HLA) class I complex. Due to these limitations, many discovery efforts focus on identifying neoepitopes from a small number of cancer neoantigens in the context of few HLA alleles. Here we describe a systematic workflow to characterize binding and presentation of neoepitopes derived from 47 shared cancer neoantigens in the context of 15 HLA alleles. Through the development of a high-throughput neoepitope-HLA binding assay, we surveyed 24,149 candidate neoepitope-HLA combinations resulting in 587 stable complexes. These data were supplemented by computational prediction that identified an additional 257 neoepitope-HLA pairs, resulting in a total of 844 unique combinations. We used these results to build sensitive targeted mass spectrometry assays to validate neoepitope presentation on a panel of HLA-I monoallelic cell lines engineered to express neoantigens of interest as a single polypeptide. Altogether, our analyses detected 84 unique neoepitope-HLA pairs derived from 37 shared cancer neoantigens and presented across 12 HLA alleles. We subsequently identified multiple TCRs which specifically recognized two of these neoantigen-HLA combinations. Finally, these novel TCRs were utilized to elicit a T cell response suggesting that these neoepitopes are likely to be immunogenic. Together these data represent a validated, extensive resource of therapeutically relevant neoepitopes and the HLA context in which they can be targeted.
Integration and segregation in the brain as a cognitive flexibility during tasks and rest

To flexibly respond to a continuously changing environment, the human brain must be able to flexibly switch amongst many demanding cognitive tasks. The flexibility inside the brain is enabled by integrating and segregating information in large-scale functional networks over time. In this study, we used graph theory metrics prior to clustering to identify two brain states, segregated and integrated, in 100 healthy adults selected from the Human Connectome Project (HCP) dataset at rest and during six cognitive tasks. Furthermore, we explored two-dimensional (2D) latent space revealed by a deep autoencoder. In the latent space, the integrated state occupied less space compared with the segregated state. After binning the latent space, we obtained entropy from the probability for each data point of being in the bin. The integrated state showed lower entropy than the segregated state, and the rest modality showed higher entropy in both states compared with tasks. We also found that modularity and global efficiency are good measures for distinguishing between tasks and rest in both states. Overall, the study shows that integration and segregation are present in rest and in task modalities, while integration serves as information compression and segregation as information specialisation. These characteristics ensure the necessary cognitive flexibility to learn new tasks with deep proficiency.
Urine-Based Detection of Biomarkers Indicative of Chronic Kidney Disease in a Patient Cohort from Ghana

Chronic kidney disease (CKD) is a global health burden with a continuously increasing prevalence associated with an increasing incidence of diabetes and hypertension in aging populations. The CKD definition of a more than three months lasting low glomerular filtration rate (GFR) or other renal impairments including proteinuria implies that multiple factors may contribute to the disease. While there are indications of ethnic differences it is hard to disentangle these from confounding social factors. Usually, CKD is detected in later stages of the disease when irreversible renal damage has already occurred, thus suggesting a need for early non-invasive diagnostic markers. In this study, we explored the urine secretome of a CKD patient cohort from Ghana employing a kidney-injury and a more general cytokine assay. We identified panels of kidney-specific cytokine markers which were also gender-specific and a panel of gender-independent cytokine markers. The gender-specific markers are IL10 and MME for male and CLU, RETN, AGER, EGFR and VEGFA for female. The gender-independent cytokine markers were APOA1, ANGPT2, C5, CFD, GH1, ICAM1, IGFBP2, IL8, KLK4, MMP9 and SPP1 (up-regulated) and FLT3LG, CSF1, PDGFA, RETN and VEGFA (down-regulated). APOA1 – the major component of HDL particles – was up-regulated in Ghanaian CKD patients and its co-occurrence with APOL1 in a subpopulation of HDL particles may point to specific CKD-predisposing APOL1 haplotypes in patients of African descent – this however needs further investigation. The identified panels may lay down the foundation for CKD-biomarker assays to be confirmed in further studies with a larger cohort of patients.
Electrically charged black hole on AdS3: Scale invariance and the Smarr formula

The Einstein-Maxwell theory with negative cosmological constant in three spacetime dimensions is considered. It is shown that the Smarr relation for the electrically charged BTZ black hole emerges from two different approaches based on the scaling symmetry of the asymptotic behaviour of the fields at infinity. In the first approach, we prove that the conservation law associated to the scale invariance of the action for a class of stationary and circularly symmetric configurations, allows to obtain the Smarr formula as long as a special set of holographic boundary conditions is satisfied. This particular set is singled out making the integrability conditions for the energy compatible with the scale invariance of the reduced action. In the second approach, it is explicitly shown that the Smarr formula is recovered through the Euler theorem for homogeneous functions, provided the same set of holographic boundary conditions is fulfilled.