Computational modelling in disorders of consciousness: Closing the gap towards personalised models for restoring consciousness.

Disorders of consciousness are complex conditions characterised by persistent loss of responsiveness due to brain injury. They present diagnostic challenges and limited options for treatment, and highlight the urgent need for a more thorough understanding of how human consciousness arises from coordinated neural activity. The increasing availability of multimodal neuroimaging data has given rise to a wide range of clinically- and scientifically-motivated modelling efforts, seeking to improve data-driven stratification of patients, to identify causal mechanisms for patient pathophysiology and loss of consciousness more broadly, and to develop simulations as a means of testing in silico potential treatment avenues to restore consciousness. As a dedicated Working Group of clinicians and neuroscientists of the international Curing Coma Campaign, here we provide our framework and vision to understand the diverse statistical and generative computational modelling approaches that are being employed in this fast-growing field. We identify the gaps that exist between the current state-of-the-art in statistical and biophysical computational modelling in human neuroscience, and the aspirational goal of a mature field of modelling disorders of consciousness; which might drive improved treatments and outcomes in the clinic. Finally, we make several recommendations for how the field as a whole can work together to address these challenges.

Perfusion Imaging Predicts Favorable Outcomes after Basilar Artery Thrombectomy.

OBJECTIVE: Perfusion imaging identifies anterior circulation stroke patients who respond favorably to endovascular thrombectomy (ET), but its role in basilar artery occlusion (BAO) is unknown. We hypothesized that BAO patients with limited regions of severe hypoperfusion (time to reach maximum concentration in seconds [Tmax] > 10) would have a favorable response to ET compared to patients with more extensive regions involved. METHODS: We performed a multicenter retrospective cohort study of BAO patients with perfusion imaging prior to ET. We prespecified a Critical Area Perfusion Score (CAPS; 0-6 points), which quantified severe hypoperfusion (Tmax > 10) in cerebellum (1 point/hemisphere), pons (2 points), and midbrain and/or thalamus (2 points). Patients were dichotomized into favorable (CAPS ≤ 3) and unfavorable (CAPS > 3) groups. The primary outcome was a favorable functional outcome 90 days after ET (modified Rankin Scale = 0-3). RESULTS: One hundred three patients were included. CAPS ≤ 3 patients (87%) had a lower median National Institutes of Health Stroke Scale score (NIHSS; 12.5, interquartile range [IQR] = 7-22) compared to CAPS > 3 patients (13%; 23, IQR = 19-36; p = 0.01). Reperfusion was achieved in 84% of all patients, with no difference between CAPS groups (p = 0.42). Sixty-four percent of reperfused CAPS ≤ 3 patients had a favorable outcome compared to 8% of nonreperfused CAPS ≤ 3 patients (odds ratio [OR] = 21.0, 95% confidence interval [CI] = 2.6-170; p < 0.001). No CAPS > 3 patients had a favorable outcome, regardless of reperfusion. In a multivariate regression analysis, CAPS ≤ 3 was a robust independent predictor of favorable outcome after adjustment for reperfusion, age, and pre-ET NIHSS (OR = 39.25, 95% CI = 1.34->999, p = 0.04). INTERPRETATION: BAO patients with limited regions of severe hypoperfusion had a favorable response to reperfusion following ET. However, patients with more extensive regions of hypoperfusion in critical brain regions did not benefit from endovascular reperfusion. ANN NEUROL 2022;91:23-32.

Central neurogenetic signatures of the visuomotor integration system.

Visuomotor impairments characterize numerous neurological disorders and neurogenetic syndromes, such as autism spectrum disorder (ASD) and Dravet, Fragile X, Prader-Willi, Turner, and Williams syndromes. Despite recent advances in systems neuroscience, the biological basis underlying visuomotor functional impairments associated with these clinical conditions is poorly understood. In this study, we used neuroimaging connectomic approaches to map the visuomotor integration (VMI) system in the human brain and investigated the topology approximation of the VMI network to the Allen Human Brain Atlas, a whole-brain transcriptome-wide atlas of cortical genetic expression. We found the genetic expression of four genes-TBR1, SCN1A, MAGEL2, and CACNB4-to be prominently associated with visuomotor integrators in the human cortex. TBR1 gene transcripts, an ASD gene whose expression is related to neural development of the cortex and the hippocampus, showed a central spatial allocation within the VMI system. Our findings delineate gene expression traits underlying the VMI system in the human cortex, where specific genes, such as TBR1, are likely to play a central role in its neuronal organization, as well as on specific phenotypes of neurogenetic syndromes.

Opposing brain differences in 16p11.2 deletion and duplication carriers.

Deletions and duplications of the recurrent ~600 kb chromosomal BP4-BP5 region of 16p11.2 are associated with a broad variety of neurodevelopmental outcomes including autism spectrum disorder. A clue to the pathogenesis of the copy number variant (CNV)'s effect on the brain is that the deletion is associated with a head size increase, whereas the duplication is associated with a decrease. Here we analyzed brain structure in a clinically ascertained group of human deletion (N = 25) and duplication (N = 17) carriers from the Simons Variation in Individuals Project compared with age-matched controls (N = 29 and 33, respectively). Multiple brain measures showed increased size in deletion carriers and reduced size in duplication carriers. The effects spanned global measures of intracranial volume, brain size, compartmental measures of gray matter and white matter, subcortical structures, and the cerebellum. Quantitatively, the largest effect was on the thalamus, but the collective results suggest a pervasive rather than a selective effect on the brain. Detailed analysis of cortical gray matter revealed that cortical surface area displays a strong dose-dependent effect of CNV (deletion > control > duplication), whereas average cortical thickness is less affected. These results suggest that the CNV may exert its opposing influences through mechanisms that influence early stages of embryonic brain development.

Structural phase transition causing anomalous photoluminescence behavior in perovskite (C6H11NH3)2[PbI4].

Optical and structural properties of the organic-inorganic hybrid perovskite-type (C6H11NH3)2[PbI4] (abbreviated as C6PbI4) were investigated using optical absorption, photoluminescence (PL), and x-ray diffraction measurements. Room temperature, optical absorption measurements, performed on spin-coated films of C6PbI4, revealed two absorption bands at 2.44 and 3.21 eV. Upon 325 nm (3.815 eV) laser irradiation, strong green PL emission peaks were observed at 2.41 eV (P1) and 2.24 eV (P2) and assigned to free and localized excitons, respectively. The exciton binding energy was estimated at 356 meV. At low temperature, two additional emission bands were detected at 2.366 eV (P3) and a large band (LB) at 1.97 eV. The former appeared only below 40 K and the latter emerged below 130 K. The thermal dependence of the PL spectra revealed an abnormal behavior accompanied by singularities in the peak positions and intensities at 40 and 130 K. X-ray diffraction studies performed on powder and single crystals as a function of temperature evidenced significant changes of the interlayer spacing at 50 K and ∼138 K. Around 138 K, a commensurate to incommensurate structural phase transition occurred on cooling. It involves a symmetry breaking leading to a distortion of the PbI6 octahedron. The resulting incommensurate spatial modulation of the Pb-I distances (and Pb-I-Pb angles) causes a spatial modulation of the band gap, which is at the origin of the emergence of the LB below ∼130 K and the anomalous behavior of the position of P1 below 130 K. The change of the interlayer spacing in the 40-50 K range may in turn be related to the significant decrease of the intensity of P2 and the maximum emission of the LB. These results underline the intricate character of the structural and the PL properties of the hybrid perovskites; understanding such properties should benefit to the design of optoelectronic devices with targeted properties.

Clusterization-Triggered Emission Enhanced by Energy Transfer in the Layered Metal Halide Hybrid Material (TET)2[Pb4Cl16].

Clusterization-triggered emission (CTE) of nonconventional chromophores has recently attracted increased interest for its synergetic photophysical properties and promising applications, such as optical anticounterfeiting, white-light emission devices, or molecular sensing. Many studies have been conducted on pure organic clusteroluminogens (CLgens), but very few have explored organic-inorganic hybrid (OIH) materials. This work deals with optical properties of a new OIH compound (TET)2[Pb4Cl16] (TET = N,N'-bis(2-aminoethyl)-1,3-propanediamine (C7N4H24)), which presents an unprecedented two-dimensional perovskitoid structure formed by strongly distorted [Pb4Cl16] layers of corner and edge-sharing [PbCl6] octahedra, separated by TET tetra-ammonium cations. Under UV-visible excitations, (TET)2[Pb4Cl16] exhibits white-light emission, tunable excitation-wavelength-dependent emission, and green afterglow room temperature phosphorescence (RTP) lasting for more than 0.63 s, all of which are direct signatures of CTE. The optical interpretations are supported by density functional theory (DFT) calculations of the band structure. Two mechanisms are involved in the emission process: resonant energy transfer (RET) between the organic and the inorganic components, and clusteroluminescence (CL) governed by a rigid conformation of the organic cations and extended electron delocalization over supramolecular organic clusters confined within the interlayer spacing. The different features of CLgens in (TET)2[Pb4Cl16] are discussed, and the role of the organic nonconjugated molecule in the emission process is emphasized.

Mapping the Unconscious Brain: Insights From Advanced Neuroimaging.

SUMMARY: Recent advances in neuroimaging have been a preeminent factor in the scientific effort to unravel mechanisms of conscious awareness and the pathophysiology of disorders of consciousness. In the first part of this review, we selectively discuss operational models of consciousness, the biophysical signal that is measured using different imaging modalities, and knowledge on disorders of consciousness that has been gleaned with each neuroimaging modality. Techniques considered include diffusion-weighted imaging, diffusion tensor imaging, different types of nuclear medicine imaging, functional MRI, magnetoencephalography, and the combined transcranial magnetic stimulation-electroencephalography approach. In the second part of this article, we provide an overview of how advanced neuroimaging can be leveraged to support neurological prognostication, the use of machine learning to process high-dimensional imaging data, potential applications in clinical practice, and future directions.

The one-dimensional organic-inorganic hybrid: catena-poly[bis-[1-(3-ammonio-prop-yl)-1H-imidazolium] [[iodidoplumbate(II)]-tri-µ-iodido-plumbate(II)-tri-µ-iodido-[iodidoplumbate(II)]-di-µ-iodido]].

The organic-inorganic hybrid, {(C(6)H(13)N(3))(2)[Pb(3)I(10)]}(n), was obtained by the reaction of 1-(3-ammonio-prop-yl)imidazolium triiodide and PbI(2) at room temperature. The structure contains one-dimensional {[Pb(3)I(10)](4-)}(n) polymeric anions spreading parallel to [001], resulting from face-face-edge association of PbI(6) distorted octa-hedra. One of the Pb(II) cations is imposed at an inversion centre, whereas the second occupies a general position. N-H⋯I hydrogen bonds connect the organic cations and inorganic anions.

Vibrational study of phase transition in N-benzyl methyl ammonium dihydrogenmonophosphate monohydrate.

Raman spectra (100-3200 cm(-1)) of polycrystalline samples of C(6)H(5)CH(2)NH(2)CH(3)H(2)PO(4).H(2)O were studied at temperature ranging from 77 to 350 K. By comparison with homologue compounds and calculated wavenumbers, an assignment of the observed bands is proposed. The thermal evolution of Raman spectra reveals an order-disorder phase transition at about 120 K involving the hydrogen bonds coupled with the distortion of the organic cations. The line at 244 cm(-1)assigned to tau(CH(3)) shows a remarkable evolution across the transition. Therefore, a careful analysis of the thermal evolution of this mode was performed using Porto model. The activation energy, obtained from the plot of Deltanu(1/2) versus temperature, is E(a)=1.27 kcal mol(-1). This value is of the same order of magnitude as the one found for homologue hydrogen bonded compounds.

The one-dimensional organic inorganic hybrid compound poly[(diethyl-ene-triamine)tetra-µ-iodido-dilead(II)].

A new organic-inorganic hybrid, [Pb(2)I(4)(C(4)H(13)N(3))](n), was obtained by the reaction of C(4)N(3)H(10) and PbI(2) at room temperature. The structure is a three-dimensional polymer resulting from the association of PbI(6) octa-hedra and a mixed lead organic-inorganic PbI(4)(C(4)N(3)H(13)) coordination polyhedron. Both Pb atoms, two I atoms and one N atom lie on a mirror plane. N-H⋯I hydrogen bonds further connect the organic unit and some I atoms.

Quantifying the Effects of 16p11.2 Copy Number Variants on Brain Structure: A Multisite Genetic-First Study.

BACKGROUND: 16p11.2 breakpoint 4 to 5 copy number variants (CNVs) increase the risk for developing autism spectrum disorder, schizophrenia, and language and cognitive impairment. In this multisite study, we aimed to quantify the effect of 16p11.2 CNVs on brain structure. METHODS: Using voxel- and surface-based brain morphometric methods, we analyzed structural magnetic resonance imaging collected at seven sites from 78 individuals with a deletion, 71 individuals with a duplication, and 212 individuals without a CNV. RESULTS: Beyond the 16p11.2-related mirror effect on global brain morphometry, we observe regional mirror differences in the insula (deletion > control > duplication). Other regions are preferentially affected by either the deletion or the duplication: the calcarine cortex and transverse temporal gyrus (deletion > control; Cohen's d > 1), the superior and middle temporal gyri (deletion < control; Cohen's d < -1), and the caudate and hippocampus (control > duplication; -0.5 > Cohen's d > -1). Measures of cognition, language, and social responsiveness and the presence of psychiatric diagnoses do not influence these results. CONCLUSIONS: The global and regional effects on brain morphometry due to 16p11.2 CNVs generalize across site, computational method, age, and sex. Effect sizes on neuroimaging and cognitive traits are comparable. Findings partially overlap with results of meta-analyses performed across psychiatric disorders. However, the lack of correlation between morphometric and clinical measures suggests that CNV-associated brain changes contribute to clinical manifestations but require additional factors for the development of the disorder. These findings highlight the power of genetic risk factors as a complement to studying groups defined by behavioral criteria.

HF, MP2 and DFT calculations and spectroscopic study of the vibrational and conformational properties of N-diethylendiamine.

The conformational stability and vibrational modes of the N-diethylendiamine organic cation (N-DD(2+)) were studied by experimental (Raman) spectroscopy combined with theoretical calculations. Various ab initio theories were used: Hartree-Fock (HF) theory, Möller-Plesset second-order perturbation (MP2) theory and density functional theory (DFT). Three stable conformers of N-DD(2+), trans-trans, gauche-gauche and gauche-trans were calculated. A comparison between the computed structural parameters of the conformers at both levels of theory and the X-ray data was made. It is demonstrated that the N-DD(2+) cation adopts more probably the gauche-gauche conformation at room temperature. In order to make a more detailed interpretation of the low temperature phase transition of N-DDHP, the Raman spectra of N-DDHP were recorded at room and low temperature in the 200-3400 cm(-1) region. The vibrational frequencies of the different conformers of N-DD(2+) were also calculated using the DFT/B3LYP (6-31G(d)) level of theory. By comparison between the experimental and theoretical results, the conformational dynamic of the N-DD(2+) organic cation was confirmed. It is shown that the N-DD(2+) cation configuration changes from gauche-gauche conformer to gauche-trans conformer when decreasing the temperature.

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one by Hartree-Fock and density functional theory calculations.

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one (C(11)H(13)N(3)O(2)) in the ground state have been investigated by Hartree-Fock and density functional method (B3LYP and BLYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of title compound and calculated results by HF and DFT methods indicate that B3LYP is superior to the scaled HF approach for molecular problems.

Structural, vibrational and ab initio studies of L-histidine oxalate.

Single crystals of L-histidine oxalate were obtained by slow evaporation of an aqueous solution at room temperature. The grown crystals have been subjected to X-ray diffraction (XRD), Infrared, and Raman spectroscopy. The title compound crystallises in the non-centrosymmetric space group P2(1)2(1)2(1,) the crystal cohesion is achieved by relatively strong hydrogen bonds, so that the NH3 groups show significant distortion with respect to the tetrahedral symmetry. Raman and infrared spectra of the title compound were recorded in the frequency range 300-3200 and 400-4000 cm-1, respectively. To obtain a reliable assignment of the observed spectral lines, we have calculated the geometry and the frequencies of the vibrational modes of histidine cation and the oxalate anion using the semi empirical PM3 method.

Crystal structure, vibrational studies and optical properties of a new organic-inorganic hybrid compound (C10H28N4)CuCl5Cl⋠4H2O.

A new organic-inorganic hybrid material, 1,4-bis(3-ammoniumpropyl) piperazinium pentachloridocuprate(II) chloride tetrahydrate [(C10H28N4)CuCl5Cl⋅4H2O], has been synthesized and characterized by X-ray diffraction, UV-visible absorption, Infrared and Raman spectroscopy. The compound crystallizes in the orthorhombic system and Pnma space group with a=8.18 (3)Å, b=10.96 (5)Å, c=21.26 (9)Å, V=2254.3 (15)Å(3). In this structure, the Cu(2+) ion, surrounded by five chlorides, adopts the square pyramidal coordination geometry. The structure of this compound consists of tetraprotonated 1,4-bis(3-ammoniumpropyl) piperazinium cations and the anionic sublattice is built up of isolated, square pyramid [CuCl5](3)(-) units, chloride ion Cl(-) and water molecules connected with each other by hydrogen bonds. Organic and inorganic entities are interconnected by means of hydrogen bonding contacts [NH⋯O(Cl), O(W)H⋯Cl and O(W)H⋯O]. Furthermore, the room temperature IR and Raman spectra of the title compound were recorded and analyzed on the basis of literature data. The optical study was also investigated by UV-Vis absorption. In fact, the organic-inorganic hybrid crystal thin film can be easily prepared by spin-coating method from the ethanol solution of the (C10H28N4)CuCl5Cl⋅4H2O hybrid compound and it showed absorptions characteristics of CuCl based layered compounds centered at 275 and 374 nm.

Fusobacterium nucleatum: an emerging bug in colorectal tumorigenesis.

The human intestinal microbiota is a plethora of diverse microbial species, wherein certain bacteria considered as driver bacteria with procarcinogenic features contribute directly toward colonic epithelium cell damage to initiate colorectal carcinogenesis. However, some bacteria, in particular Fusobacterium nucleatum, which is otherwise a normal resident of the oral microflora and a relatively poor colonizer of the healthy gut, have also been considered to play a role in the development of colorectal cancer. Many studies have reported that F. nucleatum is associated with colorectal adenomas and advanced-stage colorectal cancer, but its precise role in the early stages of colorectal tumorigenesis is poorly understood. Here, we review some of the important features of F. nucleatum, its association with inflammatory bowel disease, modulation of the tumor-immune microenvironment, and E-cadherin/ß-catenin signaling.

A mouse model suggests two mechanisms for thyroid alterations in infantile cystinosis: decreased thyroglobulin synthesis due to endoplasmic reticulum stress/unfolded protein response and impaired lysosomal processing.

Thyroid hormones are released from thyroglobulin (Tg) in lysosomes, which are impaired in infantile/nephropathic cystinosis. Cystinosis is a lysosomal cystine storage disease due to defective cystine exporter, cystinosin. Cystinotic children develop subclinical and then overt hypothyroidism. Why hypothyroidism is the most frequent and earliest endocrine complication of cystinosis is unknown. We here defined early alterations in Ctns(-/-) mice thyroid and identified subcellular and molecular mechanisms. At 9 months, T4 and T3 plasma levels were normal and TSH was moderately increased (∼4-fold). By histology, hyperplasia and hypertrophy of most follicles preceded colloid exhaustion. Increased immunolabeling for thyrocyte proliferation and apoptotic shedding indicated accelerated cell turnover. Electron microscopy revealed endoplasmic reticulum (ER) dilation, apical lamellipodia indicating macropinocytic colloid uptake, and lysosomal cystine crystals. Tg accumulation in dilated ER contrasted with mRNA down-regulation. Increased expression of ER chaperones, glucose-regulated protein of 78 kDa and protein disulfide isomerase, associated with alternative X-box binding protein-1 splicing, revealed unfolded protein response (UPR) activation by ER stress. Decreased Tg mRNA and ER stress suggested reduced Tg synthesis. Coordinated increase of UPR markers, activating transcription factor-4 and C/EBP homologous protein, linked ER stress to apoptosis. Hormonogenic cathepsins were not altered, but lysosome-associated membrane protein-1 immunolabeling disclosed enlarged vesicles containing iodo-Tg and impaired lysosomal fusion. Isopycnic fractionation showed iodo-Tg accumulation in denser lysosomes, suggesting defective lysosomal processing and hormone release. In conclusion, Ctns(-/-) mice showed the following alterations: 1) compensated primary hypothyroidism and accelerated thyrocyte turnover; 2) impaired Tg production linked to ER stress/UPR response; and 3) altered endolysosomal trafficking and iodo-Tg processing. The Ctns(-/-) thyroid is useful to study disease progression and evaluate novel therapies.

Synthesis, crystal structure, vibrational spectroscopy, optical properties and theoretical studies of a new organic-inorganic hybrid material: [((CH3)2NH2)(+)]6·[(BiBr6)(3-)]2.

A new organic-inorganic hybrid material, [((CH3)2NH2)(+)]6·[(BiBr6)(3-)]2, has been synthesized and characterized by X-ray diffraction, FT-IR, Raman spectroscopy and UV-Visible absorption. The studied compound crystallizes in the triclinic system, space group P1¯ with the following parameters: a=8.4749(6)(Å), b=17.1392(12)(Å), c=17.1392(12)(Å), α=117.339(0)°, ß=99.487(0)°, γ=99.487(0)° and Z=2. The crystal lattice is composed of a two discrete (BiBr6)(3-) anions surrounded by six ((CH3)2NH2)(+) cations. Complex hydrogen bonding interactions between (BiBr6)(3-) and organic cations from a three-dimensional network. Theoretical calculations were performed using density functional theory (DFT) for studying the molecular structure, vibrational spectra and optical properties of the investigated molecule in the ground state. The full geometry optimization of designed system is performed using DFT method at B3LYP/LanL2DZ level of theory using the Gaussian03. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from FT-IR and Raman spectra are assigned based on the results of the theoretical calculations. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental UV-Visible spectrum. The results show good consistent with the experiment and confirm the contribution of metal orbital to the HOMO-LUMO boundary.

Crystal structure, vibrational studies, optical properties and DFT calculation of bis 2-aminobenzothiazolium tetrachloridocuprate.

The zero dimensional organic-inorganic hybrid compound (C7H7N2S)2CuCl4 was synthesized and characterized by X-ray diffraction, infrared absorption, Raman spectroscopy scattering and optical transmission measurements. The title compound crystallizes in the monoclinic system with P21/c space group. The unit cell parameters are a=7.060 (5) Å, b=9.748 (5) Å, c=14.037 (5) Å, ß=98.520 (5)° and Z=2. The copper (II) ion has square planar coordination environment and the structure is built up from isolated [CuCl4](2)(-) anion surrounded by organic cations connected together via N-H⋯Cl hydrogen bonding. Room temperature IR and Raman spectra of the title compound were recorded and analyzed. The theoretical geometrical parameters in the ground state have been investigated by density functional theory (DFT) with the B3LYP/LanL2DZ level of theory. The organic-inorganic hybrid crystal thin film can be easily prepared by spin-coating method from the ethanol solution of the (C7H7N2S)2CuCl4 compound and it showed characteristic absorptions of Cu-Cl based layered perovskite centered at 288 and 400 nm.