Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image.

Inferring gene expressions from histopathological images has long been a fascinating yet challenging task, primarily due to the substantial disparities between the two modality. Existing strategies using local or global features of histological images are suffering model complexity, GPU consumption, low interpretability, insufficient encoding of local features, and over-smooth prediction of gene expressions among neighboring sites. In this paper, we develop TCGN (Transformer with Convolution and Graph-Node co-embedding method) for gene expression estimation from H&E-stained pathological slide images. TCGN comprises a combination of convolutional layers, transformer encoders, and graph neural networks, and is the first to integrate these blocks in a general and interpretable computer vision backbone. Notably, TCGN uniquely operates with just a single spot image as input for histopathological image analysis, simplifying the process while maintaining interpretability. We validate TCGN on three publicly available spatial transcriptomic datasets. TCGN consistently exhibited the best performance (with median PCC 0.232). TCGN offers superior accuracy while keeping parameters to a minimum (just 86.241 million), and it consumes minimal memory, allowing it to run smoothly even on personal computers. Moreover, TCGN can be extended to handle bulk RNA-seq data while providing the interpretability. Enhancing the accuracy of omics information prediction from pathological images not only establishes a connection between genotype and phenotype, enabling the prediction of costly-to-measure biomarkers from affordable histopathological images, but also lays the groundwork for future multi-modal data modeling. Our results confirm that TCGN is a powerful tool for inferring gene expressions from histopathological images in precision health applications.

Case report: Bilateral parotid abscess in a 54-day-old infant.

Acute parotid abscess (PA) is rare in children and is prone to occur in neonates or preterm infants with high-risk factors. Sporadic cases of unilateral PA have been reported in older children. Here, we report a case of a 54-day-old child who developed bilateral PA due to Staphylococcus aureus infection. The infant showed bilateral cervical lymphadenopathy initially following a 13-valent pneumococcal conjugate vaccine (PCV13). However, bilateral PA developed 6 h after he was diagnosed with lymphadenitis on Day 9 of illness. Rapid PA progression from cervical lymphadenitis is rare. He recovered quickly under treatment with appropriate antibiotics based on susceptibility testing and surgical incision and drainage.

Corrigendum: Tonoplast proton pumps regulate nuclear spacing of female gametophytes via mediating polar auxin transport in arabidopsis.

[This corrects the article DOI: 10.3389/fpls.2022.1006735.].

Tonoplast proton pumps regulate nuclear spacing of female gametophytes via mediating polar auxin transport in Arabidopsis.

The vacuole is an important organelle with multiple functions in plants, and the tonoplast that wraps the vacuole also plays essential roles in intracellular trafficking and ion homeostasis. Previous studies found that tonoplast proton pumps regulate embryo development and morphogenesis through their effects on vacuole biogenesis and distribution, as well as polar auxin transport and concomitant auxin gradient. However, the precise roles of the tonoplast proton pumps in gametophyte development remain unclear. Here we demonstrated that the lack of two types of tonoplast proton pumps or the absence of V-ATPase alone leads to abnormal development and nuclear localization of female gametophyte (FG), and slowed endosperm nuclei division after fertilization of the central cell. We further revealed that V-ATPase regulates auxin levels in ovules through coordinating the content and localization of PIN-FORMED 1 (PIN1) protein, hence influencing nuclear spacing between centra cell and egg cell, and subsequent endosperm development. Collectively, our findings revealed a crucial role of V-ATPase in auxin-mediated FG development in Arabidopsis and expanded our understanding of the functions of tonoplast proton pumps in seed plants reproductive development.

PIN3 positively regulates the late initiation of ovule primordia in Arabidopsis thaliana.

Ovule initiation determines the maximum ovule number and has great impact on seed number and yield. However, the regulation of ovule initiation remains largely elusive. We previously reported that most of the ovule primordia initiate asynchronously at floral stage 9 and PINFORMED1 (PIN1) polarization and auxin distribution contributed to this process. Here, we further demonstrate that a small amount of ovule primordia initiate at floral stage 10 when the existing ovules initiated at floral stage 9 start to differentiate. Genetic analysis revealed that the absence of PIN3 function leads to the reduction in pistil size and the lack of late-initiated ovules, suggesting PIN3 promotes the late ovule initiation process and pistil growth. Physiological analysis illustrated that, unlike picloram, exogenous application of NAA can't restore these defective phenotypes, implying that PIN3-mediated polar auxin transport is required for the late ovule initiation and pistil length. qRT-PCR results indicated that the expression of SEEDSTICK (STK) is up-regulated under auxin analogues treatment while is down-regulated in pin3 mutants. Meanwhile, overexpressing STK rescues pin3 phenotypes, suggesting STK participates in PIN3-mediated late ovule initiation possibly by promoting pistil growth. Furthermore, brassinosteroid influences the late ovule initiation through positively regulating PIN3 expression. Collectively, this study demonstrates that PIN3 promotes the late ovule initiation and contributes to the extra ovule number. Our results give important clues for increasing seed number and yield of cruciferous and leguminous crops.

Case Report: Fatal Neurotoxicity Following Resmethrin Poisoning in a Child.

Resmethrin, a type I pyrethroid insecticide, can activate sodium channels, causing neurotoxicity in both mammals and insects. Possible routes of poisoning include inhalation, dermal contact and ingestion. There are no specific symptoms for resmethrin poisoning. Until now, no antidote has been available for resmethrin. Resmethrin poisoning is rarely reported in children. Here, we report a fatal case of resmethrin poisoning that might have been caused by accidental ingestion by a 26-month-old child. He presented with neurotoxic symptoms that included vomiting, recurrent seizures, and coma. The cranial CT showed extensive lesions of low intensity in the bilateral white matter, thalamus, brainstem, and cerebellum. Lumbar punctures showed increased intracranial pressure (ICP > 25 mmHg). Cerebrospinal fluid (CSF) tests revealed that protein was elevated to 289.2 mg/dL without pleocytosis. Resmethrin was detected in his blood by liquid chromatography-mass spectrometry, which confirmed the diagnosis of resmethrin poisoning. The child developed brain stem herniation and then was declared brain dead at the 77th h after admission. Resmethrin poisoning can be fatal, and it requires immediate diagnosis and treatment. Previous studies reported that cranial CT and CSF analyses were all normal in patients with pyrethroid poisoning. This case might extend the knowledge of neuroimaging and CSF analysis in children with resmethrin poisoning.

Intercalated architecture of MA2Z4 family layered van der Waals materials with emerging topological, magnetic and superconducting properties.

The search for new two-dimensional monolayers with diverse electronic properties has attracted growing interest in recent years. Here, we present an approach to construct MA2Z4 monolayers with a septuple-atomic-layer structure, that is, intercalating a MoS2-type monolayer MZ2 into an InSe-type monolayer A2Z2. We illustrate this unique strategy by means of first-principles calculations, which not only reproduce the structures of MoSi2N4 and MnBi2Te4 that were already experimentally synthesized, but also predict 72 compounds that are thermodynamically and dynamically stable. Such an intercalated architecture significantly reconstructs the band structures of the constituents MZ2 and A2Z2, leading to diverse electronic properties for MA2Z4, which can be classified according to the total number of valence electrons. The systems with 32 and 34 valence electrons are mostly semiconductors. Whereas, those with 33 valence electrons can be nonmagnetic metals or ferromagnetic semiconductors. In particular, we find that, among the predicted compounds, (Ca,Sr)Ga2Te4 are topologically nontrivial by both the standard density functional theory and hybrid functional calculations. While VSi2P4 is a ferromagnetic semiconductor and TaSi2N4 is a type-I Ising superconductor. Moreover, WSi2P4 is a direct gap semiconductor with peculiar spin-valley properties, which are robust against interlayer interactions. Our study thus provides an effective way of designing septuple-atomic-layer MA2Z4 with unusual electronic properties to draw immediate experimental interest.

Computation and data driven discovery of topological phononic materials.

The discovery of topological quantum states marks a new chapter in both condensed matter physics and materials sciences. By analogy to spin electronic system, topological concepts have been extended into phonons, boosting the birth of topological phononics (TPs). Here, we present a high-throughput screening and data-driven approach to compute and evaluate TPs among over 10,000 real materials. We have discovered 5014 TP materials and grouped them into two main classes of Weyl and nodal-line (ring) TPs. We have clarified the physical mechanism for the occurrence of single Weyl, high degenerate Weyl, individual nodal-line (ring), nodal-link, nodal-chain, and nodal-net TPs in various materials and their mutual correlations. Among the phononic systems, we have predicted the hourglass nodal net TPs in TeO3, as well as the clean and single type-I Weyl TPs between the acoustic and optical branches in half-Heusler LiCaAs. In addition, we found that different types of TPs can coexist in many materials (such as ScZn). Their potential applications and experimental detections have been discussed. This work substantially increases the amount of TP materials, which enables an in-depth investigation of their structure-property relations and opens new avenues for future device design related to TPs.

Fulminant encephalopathy in a child with hyperferritinemic sepsis: a case report.

BACKGROUND: Sepsis-associated encephalopathy (SAE) is epidemic in intensive care units and recognized as a fatal complication of sepsis. SAE is characterized by diffuse brain dysfunction and the correct diagnosis of SAE requires ruling out direct central nervous system (CNS) infection or other types of encephalopathy, such as hepatic encephalopathy, pulmonary encephalopathy, and other encephalopathy. CASE PRESENTATION: We reported a rare case of a 5-year-old girl who presented with abdominal pain, vomiting, recurrent seizures, and coma. Brain magnetic resonance imaging (MRI) showed diffuse white matter abnormalities in the brain on day 1. Cerebrospinal fluid (CSF) tests revealed that protein levels and glucose levels were normal without pleocytosis. CSF PCRs for pathogens were all negative. The electroencephalography examination demonstrated diffuse, generalized and slow background activity. The patient showed the symptom of hyperferritinemic sepsis with multiple organ dysfunction syndrome (MODS). SAE was also diagnosed by ruling out other encephalitis or encephalopathy. The patient made marked improvements of clinical symptoms and the lesions on brain imaging disappeared completely within two months after appropriate treatment including antibiotic treatments, methylprednisolone, intravenous immunoglobulin, membrane-based therapeutic plasma exchange (TPE), and continuous renal replacement therapy (CRRT). CONCLUSIONS: SAE can be a fatal complication of sepsis which asks for immediate diagnosis and treatment. Few reports have focus on MRI imaging findings on the early onset of hyperferritinemic sepsis with MODS since these children were too ill to undergo an MRI scan. However, SAE might appear before other systemic features of sepsis are obvious, and MRI could show abnormal lesion in the brain during the early course. Therefore, MRI should be performed early to diagnose this fatal complication which would play important roles in improving the clinical outcomes by early initiation with appropriate treatments.

[Association of YKL-40 in bronchoalveolar lavage fluid with airway damage in children with Mycoplasma pneumoniae pneumonia].

OBJECTIVE: To investigate the association of YKL-40 in bronchoalveolar lavage fluid (BALF) with airway damage in children with Mycoplasma pneumoniae pneumonia (MPP). METHODS: A total of 60 children with MPP who were admitted to the hospital were enrolled as the MPP group, and 12 children with bronchial foreign bodies were enrolled as the control group. According to the imaging findings, the MPP group was further divided into 3 subgroups: pulmonary patchy shadow (n=34), pulmonary consolidation (n=19) and pulmonary ground-glass opacity (n=7). According to the bronchoscopic findings, the MPP group was further divided into 3 subgroups: mucosal congestion/edema (n=38), mucous secretion (n=18) and plastic bronchitis (n=4). The clinical manifestations and laboratory characteristics of the children with MPP were analyzed, the expression of YKL-40 in BALF was measured. RESULTS: The MPP group had significantly higher levels of serum lactate dehydrogenase and BALF YKL-40 than the control group (P<0.05). The pulmonary consolidation subgroup had significantly higher levels of serum C-reactive protein and lactate dehydrogenase than the pulmonary patchy shadow subgroup (P<0.05), and the pulmonary consolidation and pulmonary ground-glass opacity subgroups had a significantly higher level of BALF YKL-40 than the pulmonary patchy shadow subgroup (P<0.05). The plastic bronchitis subgroup had a significantly higher level of BALF YKL-40 than the mucous secretion and mucosal congestion/edema subgroups (P<0.05). The mucous secretion and plastic bronchitis subgroups had a significantly higher proportion of children with shortness of breath than the mucosal congestion/edema subgroup (P<0.05). The plastic bronchitis subgroup had significantly higher serum levels of C-reactive protein and lactate dehydrogenase than the mucosal congestion/edema subgroup (P<0.05). CONCLUSIONS: The level of BALF YKL-40 is associated with airway damage and disease severity in children with MPP.

Underlying Topological Dirac Nodal Line Mechanism of the Anomalously Large Electron-Phonon Coupling Strength on a Be (0001) Surface.

Beryllium has recently been discovered to harbor a Dirac nodal line (DNL) in its bulk phase and the DNL-induced nontrivial surface states (DNSSs) on its (0001) surface, rationalizing several already-existing historic puzzles [Phys. Rev. Lett. 117, 096401 (2016)PRLTAO0031-900710.1103/PhysRevLett.117.096401]. However, to date the underlying mechanism as to why its (0001) surface exhibits an anomalously large electron-phonon coupling effect (λ_{e-ph}^{s}≈1.0) remains unresolved. Here, by means of first-principles calculations, we show that the coupling of the DNSSs with the phononic states mainly contributes to its novel surface e-ph enhancement. Besides the fact that the experimentally observed λ_{e-ph}^{s} and the main Eliashberg coupling function (ECF) peaks are reproduced well in our current calculations, we decompose the ECF α^{2}F(k,q;v) and the e-ph coupling strength λ(k,q;v) as a function of each electron momentum (k), each phonon momentum (q), and each phonon mode (v), evidencing the robust connection between the DNSSs and both α^{2}F(k,q;v) and λ(k,q;v). The results reveal the strong e-ph coupling between the DNSSs and the phonon modes, which contributes over 80% of the λ_{e-ph}^{s} coefficient on the Be (0001) surface. It highlights that the anomalously large e-ph coefficient on the Be (0001) surface can be attributed to the presence of its DNL-induced DNSSs, clarifying the long-debated mechanism.

Tunable metal-insulator transition, Rashba effect and Weyl Fermions in a relativistic charge-ordered ferroelectric oxide.

Controllable metal-insulator transitions (MIT), Rashba-Dresselhaus (RD) spin splitting, and Weyl semimetals are promising schemes for realizing processing devices. Complex oxides are a desirable materials platform for such devices, as they host delicate and tunable charge, spin, orbital, and lattice degrees of freedoms. Here, using first-principles calculations and symmetry analysis, we identify an electric-field tunable MIT, RD effect, and Weyl semimetal in a known, charge-ordered, and polar relativistic oxide Ag2BiO3 at room temperature. Remarkably, a centrosymmetric BiO6 octahedral-breathing distortion induces a sizable spontaneous ferroelectric polarization through Bi3+/Bi5+ charge disproportionation, which stabilizes simultaneously the insulating phase. The continuous attenuation of the Bi3+/Bi5+ disproportionation obtained by applying an external electric field reduces the band gap and RD spin splitting and drives the phase transition from a ferroelectric RD insulator to a paraelectric Dirac semimetal, through a topological Weyl semimetal intermediate state. These findings suggest that Ag2BiO3 is a promising material for spin-orbitonic applications.

Dirac Node Lines in Pure Alkali Earth Metals.

Beryllium is a simple alkali earth metal, but has been the target of intensive studies for decades because of its unusual electron behavior at surfaces. The puzzling aspects include (i) severe deviations from the description of the nearly free-electron picture, (ii) an anomalously large electron-phonon coupling effect, and (iii) giant Friedel oscillations. The underlying origins for such anomalous surface electron behavior have been under active debate, but with no consensus. Here, by means of first-principles calculations, we discover that this pure metal system, surprisingly, harbors the Dirac node line (DNL) that in turn helps to rationalize many of the existing puzzles. The DNL is featured by a closed line consisting of linear band crossings, and its induced topological surface band agrees well with previous photoemission spectroscopy observations on the Be (0001) surface. We further reveal that each of the elemental alkali earth metals of Mg, Ca, and Sr also harbors the DNL and speculate that the fascinating topological property of the DNL might naturally exist in other elemental metals as well.

Stable compositions and structures in the Na-Bi system.

At P = 1 atm, the only stable compounds in the Na-Bi binary system are Na3Bi and NaBi, which have recently been discovered to exhibit intriguing electronic behaviour as a 3D topological Dirac semimetal and a topological metal, respectively. By means of first-principles calculations coupled with evolutionary structural searches, we have systematically investigated the phase stabilities, the crystal structures and the corresponding electronic properties of the binary Na-Bi system. At ambient pressure, our calculations have reproduced well the experimentally observed compositions and structures of Na3Bi and NaBi. At high pressures, we have found that Na3Bi is transformed from the ground-state hexagonal hP24 phase to a cubic cF16 phase above 0.8 GPa, confirming previous experiments, and then to a conventional band-insulating oC16 phase above 118 GPa. The cubic cF16 phase would exhibit novel topological band ordering similar to that in HgTe. The topological metal NaBi has also been found to undergo a structural phase transition from the ambient tetragonal tP2 to a cubic cP2 structure above 36 GPa. Four compounds never before reported, Na6Bi, Na4Bi, Na2Bi and NaBi2, with new compositions, have been predicted to be experimentally synthesizable over a wide range of pressures starting at 142.5 GPa, 105 GPa, 38 GPa and 171 GPa, respectively. Moreover, a common charge transfer from Na to Bi has been observed for all compounds, but substantial interstitial charge localization in Na atomic cages has been noticed only in two compounds, Na6Bi and Na4Bi, and may be associated with close-packed Na environments.

Topological metal of NaBi with ultralow lattice thermal conductivity and electron-phonon superconductivity.

By means of first-principles and ab initio tight-binding calculations, we found that the compound of NaBi is a three-dimensional non-trivial topological metal. Its topological feature can be confirmed by the presence of band inversion, the derived effective Z2 invariant and the non-trivial surface states with the presence of Dirac cones. Interestingly, our calculations further demonstrated that NaBi exhibits the uniquely combined properties between the electron-phonon coupling superconductivity in nice agreement with recent experimental measurements and the obviously anisotropic but extremely low thermal conductivity. The spin-orbit coupling effects greatly affect those properties. NaBi may provide a rich platform to study the relationship among metal, topology, superconductivity and thermal conductivity.

First-principles study of ground-state properties of U2Mo.

By means of first-principles calculations, we have systematically investigated the structural, elastic, vibrational, thermal and electronic properties of the ground-state phase for the intermetallic compound U2Mo. Our results reveal that the previously synthesized I4/mmm structure of U2Mo is a metastable phase and unstable, neither thermodynamically nor vibrationally at the ground state. In combination with the evolutionary structural searches, our first-principles calculations suggest a new ground-state Pmmn phase, which has been confirmed theoretically to be stable, both thermodynamically and vibrationally. Moreover, through the DFT + D technique we have discussed the influence of van der Waals interactions on the structural, elastic and vibrational properties, revealing a weak effect in pure U and Mo solids and U2Mo alloy. The analysis of the electronic band structures evidences its electronic stabilities with the appearance of a deep valley in the density of states at the Fermi level. Moreover, we have investigated further the temperature-dependent structural, thermal expansion and elastic properties of our proposed Pmmn ground-state phase. These results are expected to stimulate further experimental investigations of the ground-state phase of U2Mo.

[Survey of health status and healthcare service demand of perimenopausal women in Guangdong].

OBJECTIVE: To understand the health status and healthcare service demand of perimenopausal women in Guangdong Province so as to explore the mode and methods for implementing climacteric and senectitude healthcare. METHOD: Using the method of stratified and cluster sampling and according to the geographical features of Guangdong Province, we selected 4 500 perimenopausal women aged 40-65 years from 5 relatively small cities (representatives of the urban areas) and 4 counties (representatives of the rural areas) for this survey. RESULTS: The average age of natural menopause was 48.6 years in this cohort of women, and was 48.9 years in women from the urban areas and 48.3 years in those from the rural areas. The total incidence of diseases was similar in the urban and rural areas (38.5% vs 39.5%), accounting for an incidence of 39% in the total subjects. The 6 most prevalent diseases were bone and joint disease (12.5%), hypertension (9.2%), myoma of the uterus (6.8%), gastric or duodenal ulcer (5.2%), cardiac disease (2.7%) and diabetes mellitus (2.2%). In bone and joint disease, knee joint disease and lumbar vertebrae disease were the commonest (34.3% vs 32.8%), and the incidence of bone fracture was 2.5%. Perimenopausal syndrome had a prevalence rate of 68.1%, and the most distressful symptoms were sleeplessness, muscular, bone and joint pain, fidgety, dizziness, of which 86.8% were mental symptoms and 86.0% body symptoms. Women(71.2%) with perimenopausal symptoms received no medical treatment, and only 20.5% had ever sought medical care in the department of obstetrics and gynecology, often taking traditional Chinese medicines (53.9%). Only 1.4% of the symptomatic women received hormone therapy, the rate varied from 1.0% in the rural areas to 1.8% in the urban areas. CONCLUSION: Perimenopausal syndrome and its related diseases severely affect the physical and mental health of perimenopausal women, who demand extensive healthcare services.