OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

AlphaFold2 revolutionized structural biology with the ability to predict protein structures with exceptionally high accuracy. Its implementation, however, lacks the code and data required to train new models. These are necessary to (1) tackle new tasks, like protein-ligand complex structure prediction, (2) investigate the process by which the model learns and (3) assess the model's capacity to generalize to unseen regions of fold space. Here we report OpenFold, a fast, memory efficient and trainable implementation of AlphaFold2. We train OpenFold from scratch, matching the accuracy of AlphaFold2. Having established parity, we find that OpenFold is remarkably robust at generalizing even when the size and diversity of its training set is deliberately limited, including near-complete elisions of classes of secondary structure elements. By analyzing intermediate structures produced during training, we also gain insights into the hierarchical manner in which OpenFold learns to fold. In sum, our studies demonstrate the power and utility of OpenFold, which we believe will prove to be a crucial resource for the protein modeling community.

Diagnostic significance of cerebrospinal fluid flow cytometry in Chinese children with B lineage acute lymphoblastic leukemia.

BACKGROUND: Central nervous system leukemia (CNSL) is one of the major causes of the poor prognosis of childhood leukemia. We aimed to compare the sensitivity of cytomorphology (CM) and flow cytometry (FCM) in diagnosing CNSL, emphasizing the importance of FCM in the diagnosis process. METHODS: One-hundred-sixty-five children with newly diagnosed B-cell Acute Lymphoblastic Leukemia (B-cell ALL) were included in this study. Cerebrospinal fluid (CSF) samples were taken for routine CSF analysis, CM analysis, and FCM examination. Computed tomography scans and/or magnetic resonance imaging were performed at diagnosis. Patients with CNS2, CNS3, and traumatic lumbar puncture (TLP) at diagnosis received two additional courses of triple intrathecal injections during induction treatment. We compared the sensitivity of FCM and CM in the diagnosis of children with CNSL. RESULTS: One hundred and twenty-eight (77.58%) CSF samples were negative by either CM or FCM (CM-/FCM-), four (2.42%) were positive by both CM and FCM (CM+/FCM+), and thirty-three (20%) displayed a single positive finding by FCM (CM-/FCM+) (p = 0.044). By adding two intrathecal injections in the induction treatment, ten children with TLP+ had no CNS relapse, like those with TLP-. However, compared to CNS1 and TLP, the event-free survival (EFS) did not significantly improve in patients with CNS2 and CNS3. Moreover, CNSL status was associated with worse 3-year EFS (p < 0.05). CONCLUSIONS: We have validated that FCM is more accurate in stratifying the status of the CNS compared to CM analysis. However, to improve the EFS rate of childhood leukemia, it is necessary to combine CM examination, FCM, and cranial imaging for the early diagnosis of CNSL.

Spatial and temporal patterns of above- and below- ground biomass over the Tibet Plateau grasslands and their sensitivity to climate change.

The sensitivity of grassland above- (AGB, gC m-2) and below-ground biomass (BGB, gC m-2) to climate has been shown to be significant on the Tibetan Plateau, however, the spatial patterns and sensitivity of biomass with altitudinal change needs to be quantitated. In this study, large data sets of AGB and BGB during the peak growth season, and the corresponding geographical and climate conditions in the grasslands of the Tibetan Plateau between 2001 and 2020 were analyzed, and modelled using a Cubist regression trees algorithm. The mean values for AGB and BGB were 61.3 and 1304.3 gC m-2, respectively, for the whole region over the two decades. There was a significant change in spatial AGB of 64.8 % on the Plateau (P < 0.05, with areas where AGB increased being twice as large as areas where AGB decreased), while BGB did not change significantly in majority the of the region (≥ 90.1 %, P > 0.05). In general, the areas where AGB showed positive partial correlations with precipitation were larger than the areas where AGB had positive correlations with temperature (P < 0.05). However, these trends varied depending on the climatic conditions: in the wetter regions, temperature had a greater effect on the size of the areas with positive AGB responses than precipitation (P < 0.05), while precipitation had a greater effect on the size of areas with positive BGB changes than temperature (P < 0.05). In the drier areas, however, precipitation affected the AGB response significantly compared to temperature (P < 0.05), while temperature influenced the BGB response greater than precipitation (P < 0.05). The response and sensitivity of grassland biomass to temperature and precipitation varied according to the altitude of the Plateau: the response and sensitivity were stronger and more sensitive at medium altitudes, and weak at the higher or lower altitudes. Likely, this phenomenon was resulted from the natural selection of plants to maintain the efficient use of resources during un-favourable and stressed conditions for maximum plant development and growth. These findings will help assess the ecological consequences of global climate change for the grasslands of the Tibetan Plateau, particularly in those regions with highly variable altitudes.

Core-shell structured lignin-stabilized silver nanoprisms for colorimetric detection of sulfur ions.

Widespread occurrence of sulfides in domestic and industrial wastewater contributes to environmental pollution and poses risks to human health. Therefore, the development of highly selective, sensitive, and rapid sulfur ion (S2-) detection probes in aquatic ecosystems is of paramount importance. In this study, lignin-stabilized silver nanoprisms (EHL@AgNPRs) were prepared using the seed growth and self-assembly methods. Based on this, a novel, high-performance, and environmentally friendly S2- colorimetric detection method was proposed. Lignin is believed to coat the surface of AgNPRs through cation-π and electrostatic interactions, acting as an excellent dispersant and stabilizer to prevent aggregation and shape deformation. This allows AgNPRs to maintain localized surface plasmon resonance (LSPR) characteristics and superior colorimetric sensing sensitivity towards S2- even after 30 d. The EHL@AgNPRs exhibited remarkable selectivity towards S2- with a minimum detection limit of 41.3 nM. The conjugation of lignin with AgNPRs offers a highly promising approach for the rapid detection of S2- in natural aquatic environments and for the valorization of lignin.

Shaping immune landscape of colorectal cancer by cholesterol metabolites.

Cancer immunotherapies have achieved unprecedented success in clinic, but they remain largely ineffective in some major types of cancer, such as colorectal cancer with microsatellite stability (MSS CRC). It is therefore important to study tumor microenvironment of resistant cancers for developing new intervention strategies. In this study, we identify a metabolic cue that determines the unique immune landscape of MSS CRC. Through secretion of distal cholesterol precursors, which directly activate RORγt, MSS CRC cells can polarize T cells toward Th17 cells that have well-characterized pro-tumor functions in colorectal cancer. Analysis of large human cancer cohorts revealed an asynchronous pattern of the cholesterol biosynthesis in MSS CRC, which is responsible for the abnormal accumulation of distal cholesterol precursors. Inhibiting the cholesterol biosynthesis enzyme Cyp51, by pharmacological or genetic interventions, reduced the levels of intratumoral distal cholesterol precursors and suppressed tumor progression through a Th17-modulation mechanism in preclinical MSS CRC models. Our study therefore reveals a novel mechanism of cancer-immune interaction and an intervention strategy for the difficult-to-treat MSS CRC.

LRP12 is an endogenous transmembrane inactivator of α4 integrins.

Dynamic regulation of integrin activation and inactivation is critical for precisely controlled cell adhesion and migration in physiological and pathological processes. The molecular basis for integrin activation has been intensively studied; however, the understanding of integrin inactivation is still limited. Here, we identify LRP12 as an endogenous transmembrane inhibitor for α4 integrin activation. The LRP12 cytoplasmic domain directly binds to the integrin α4 cytoplasmic tail and inhibits talin binding to the ß subunit, thus keeping integrin inactive. In migrating cells, LRP12-α4 interaction induces nascent adhesion (NA) turnover at the leading-edge protrusion. Knockdown of LRP12 leads to increased NAs and enhanced cell migration. Consistently, LRP12-deficient T cells show an enhanced homing capability in mice and lead to aggravated chronic colitis in a T cell-transfer colitis model. Altogether, LRP12 is a transmembrane inactivator for integrins that inhibits α4 integrin activation and controls cell migration by maintaining balanced NA dynamics.

Machine learning of pair-contact process with diffusion.

The pair-contact process with diffusion (PCPD), a generalized model of the ordinary pair-contact process (PCP) without diffusion, exhibits a continuous absorbing phase transition. Unlike the PCP, whose nature of phase transition is clearly classified into the directed percolation (DP) universality class, the model of PCPD has been controversially discussed since its infancy. To our best knowledge, there is so far no consensus on whether the phase transition of the PCPD falls into the unknown university classes or else conveys a new kind of non-equilibrium phase transition. In this paper, both unsupervised and supervised learning are employed to study the PCPD with scrutiny. Firstly, two unsupervised learning methods, principal component analysis (PCA) and autoencoder, are taken. Our results show that both methods can cluster the original configurations of the model and provide reasonable estimates of thresholds. Therefore, no matter whether the non-equilibrium lattice model is a random process of unitary (for instance the DP) or binary (for instance the PCP), or whether it contains the diffusion motion of particles, unsupervised learning can capture the essential, hidden information. Beyond that, supervised learning is also applied to learning the PCPD at different diffusion rates. We proposed a more accurate numerical method to determine the spatial correlation exponent [Formula: see text], which, to a large degree, avoids the uncertainty of data collapses through naked eyes.

Practical guide to using Kendall's τ in the context of forecasting critical transitions.

Recent studies demonstrate that trends in indicators extracted from measured time series can indicate an approach of an impending transition. Kendall's τ coefficient is often used to study the trend of statistics related to the critical slowing down phenomenon and other methods to forecast critical transitions. Because statistics are estimated from time series, the values of Kendall's τ are affected by parameters such as window size, sample rate and length of the time series, resulting in challenges and uncertainties in interpreting results. In this study, we examine the effects of different parameters on the distribution of the trend obtained from Kendall's τ, and provide insights into how to choose these parameters. We also suggest the use of the non-parametric Mann-Kendall test to evaluate the significance of a Kendall's τ value. The non-parametric test is computationally much faster compared with the traditional parametric auto-regressive, moving-average model test.

Transfer learning of phase transitions in percolation and directed percolation.

The latest advances of statistical physics have shown remarkable performance of machine learning in identifying phase transitions. In this paper, we apply domain adversarial neural network (DANN) based on transfer learning to studying nonequilibrium and equilibrium phase transition models, which are percolation model and directed percolation (DP) model, respectively. With the DANN, only a small fraction of input configurations (two-dimensional images) needs to be labeled, which is automatically chosen, to capture the critical point. To learn the DP model, the method is refined by an iterative procedure in determining the critical point, which is a prerequisite for the data collapse in calculating the critical exponent ν_{⊥}. We then apply the DANN to a two-dimensional site percolation with configurations filtered to include only the largest cluster which may contain the information related to the order parameter. The DANN learning of both models yields reliable results which are comparable to the ones from Monte Carlo simulations. Our study also shows that the DANN can achieve quite high accuracy at much lower cost, compared to the supervised learning.

Effect of Long-Term Fertilization on Aggregate Size Distribution and Nutrient Accumulation in Aeolian Sandy Soil.

Soil aggregates are the material basis of soil structure and important carriers of nutrients. Long-term application of organic and inorganic fertilizers can affect the composition of soil aggregates to varying degrees, which in turn affects the distribution and storage of soil nutrients. We report the results of a 15-year long-term field-based test of aeolian sandy soil and used the wet sieve method to analyze the stability of water-stable aggregates, as well as the distribution characteristics of nutrients in different particle size aggregates. Our results show that long-term application of organic fertilizer (M3) and combined organic−inorganic treatments (NPK1-M1, NPK1-M2, and NPK1-M3) help to increase the amount of organic carbon, inorganic carbon, and cation exchange in the macro-aggregates, and the improvement rates are 92−103%, 8−28%, and 74−85%, respectively. The organic content of the fertilizers also promotes the formation of macro-aggregates, and the stability of aggregates increase from 0.24 to 0.45. In contrast, the application of inorganic fertilizers (NPK1, NPK2, and NPK3) has no marked effect on the formation and stability of macro-aggregates; the application of inorganic fertilizers can merely maintain the organic carbon content of the soil. Correlation analysis shows that the application of organic fertilizers and chemical (inorganic) fertilizers containing phosphorus and potassium can markedly increase the content and reserves of available phosphorus and potassium across all aggregate sizes, and there is a significant positive correlation between these parameters and the amount of applied fertilizer (p < 0.05). Aggregates of various sizes in aeolian sandy soils in arid areas have the potential for greater nutrient storage. Therefore, organic fertilizers can be used in the agricultural production process to improve soil structure and fertility.

Targeting lysophospholipid acid receptor 1 and ROCK kinases promotes antiviral innate immunity.

Growing evidence indicates the vital role of lipid metabolites in innate immunity. The lipid lysophosphatidic acid (LPA) concentrations are enhanced in patients upon HCV or SARS-CoV-2 infection, but the function of LPA and its receptors in innate immunity is largely unknown. Here, we found that viral infection promoted the G protein­coupled receptor LPA1 expression, and LPA restrained type I/III interferon production through LPA1. Mechanistically, LPA1 signaling activated ROCK1/2, which phosphorylated IRF3 Ser97 to suppress IRF3 activation. Targeting LPA1 or ROCK in macrophages, fibroblasts, epithelial cells, and LPA1 conditional KO mice promoted interferon-induced clearance of multiple viruses. LPA1 was colocalized with the receptor ACE2 in lung and intestine. Together with previous findings that LPA1 and ROCK1/2 promoted vascular leaking or lung fibrosis, we propose that the current available preclinical drugs targeting the LPA1-ROCK module might protect from SARS-CoV-2 or various virus infections in the intestine or lung.

Integrin αEß7+ T cells direct intestinal stem cell fate decisions via adhesion signaling.

Intestinal stem cell (ISC) differentiation is regulated precisely by a niche in the crypt, where lymphocytes may interact with stem and transient amplifying (TA) cells. However, whether and how lymphocyte-stem/TA cell contact affects ISC differentiation is largely unknown. Here, we uncover a novel role of T cell-stem/TA cell contact in ISC fate decisions. We show that intestinal lymphocyte depletion results in skewed ISC differentiation in mice, which can be rescued by T cell transfer. Mechanistically, integrin αEß7 expressed on T cells binds to E-cadherin on ISCs and TA cells, triggering E-cadherin endocytosis and the consequent Wnt and Notch signaling alterations. Blocking αEß7-E-cadherin adhesion suppresses Wnt signaling and promotes Notch signaling in ISCs and TA cells, leading to defective ISC differentiation. Thus, αEß7+ T cells regulate ISC differentiation at single-cell level through cell-cell contact-mediated αEß7-E-cadherin adhesion signaling, highlighting a critical role of the T cell-stem/TA cell contact in maintaining intestinal homeostasis.

Solubility Enhancement of Ibuprofen by Adsorption onto Spherical Porous Calcium Silicate.

The solubility of a drug is higher when it is in an amorphous form than when it is in a crystalline form. To enhance the solubility of ibuprofen (IBU), a poorly water-soluble drug, we attempted to adsorb IBU onto spherical porous calcium silicate (Florite® PS300, PS300) in two ways: the evaporation (EV) and sealed heating (SH) methods. The crystallinity of the samples was evaluated using powder X-ray diffraction analysis (PXRD) and differential scanning calorimetry (DSC). The molecular interaction between IBU and PS300 was evaluated with FTIR. In addition, the dissolution behavior of IBU in the samples was assessed by the dissolution test. Based on the results of the PXRD and DSC measurements, both methods allowed adsorption of IBU onto PS300, and IBU was amorphized. Based on the FTIR observations, in the SH or EV mixtures containing 10% and 30% IBU, respectively, it seemed that the IBU molecules intermolecularly interacted with calcium molecules as the main component of PS300. Improvement in the solubility of IBU was observed with both methods; however, the dissolution rate of IBU from samples prepared via SH was higher than that from EV, or of IBU crystals. Collectively, our findings indicate that the petal-like structure of PS300, which has a spherical shape and good flowability, is an effective tool for adsorbing IBU onto PS300 via SH.

Case Report: Myeloid Sarcoma Development During Treatment for B Cell Lymphoblastic Lymphoma in a Boy with KRAS/NRAS Gene Mutations.

Here, we report a rare case of a 12-year-old boy who was initially diagnosed with B cell lymphoblastic lymphoma (BLBL) and developed myeloid sarcoma (MS) eight months after chemotherapy. Next-generation sequencing (NGS) showed mutations of KRAS and NRAS genes in both the bone marrow and lymph node. He presented an abnormal karyotype of 46, XY, -9, der (16) t (9; 16) (q13; q12), +mar. He received chemotherapy according to the South China Children's Leukemia Group 2016 protocol. Complete remission was achieved by the 15th day post-treatment. Eight months later and immediately prior to the start of maintenance therapy, the patient developed fever, skin nodules in both upper arms, and enlargement of bilateral testes. Pathological analysis of skin and testicular biopsies suggested the diagnosis of myeloid sarcoma (MS). Again, NGS examination showed mutations of KRAS and NRAS genes. The patient underwent haploidentical hematopoietic stem cell transplantation but unfortunately did not survive. The interval of eight-month interval between the initial disease onset and MS brings into question whether MS developed as part of the initial onset of disease or as a secondary tumor in association with chemotherapy. Thus, understanding the pathogenesis of MS involving abnormalities of lymphoid progenitors may assist in the prediction of prognosis and development of novel target therapies.

Concomitant Distal Tibia-Fibula Fractures Treated with Intramedullary Nailing, With or Without Fibular Fixation: A Meta-Analysis.

There is no consensus on whether a fibular fracture should be fixed when a concurrent extra-articular distal tibia fracture is managed with intramedullary nails. We evaluated the use of fibular fixation in a meta-analysis of randomized trials and observational studies. Two researchers independently assessed the quality of eligible studies and extracted the data. We analyzed 4 trials with a pooled sample of 283 patients (mean age, 24 to 43 years; 141 men), 94 who had undergone fibular fixation and 189 who had not. Two randomized trials assessed on the Cochrane risk-assessment criteria were determined to have a moderate risk of bias, and 2 retrospective cohort studies evaluated with the Newcastle-Ottawa Scale were considered to be high quality. Tibia malalignment at follow-up times ranging from 12 to 72 weeks was reported in 20% (19/94) of patients in the fibular-fixation group and 67% (126/189) of patients in the nonfixation group, indicating that fibular fixation was significantly associated with a lower risk of malalignment (risk ratio, 0.34; 95% confidence interval [CI] 0.13 to 0.92; p = .03). The groups did not differ in the proportion of patients with malalignment immediately after surgery, delayed union, nonunion, or infection. When distal extra-articular tibia-fibular fractures are treated with intramedullary nails, fibular fixation may decrease the risk of late malalignment. Further randomized controlled trials with higher quality are required to verify the result.

Data-driven identification of reliable sensor species to predict regime shifts in ecological networks.

Signals of critical slowing down are useful for predicting impending transitions in ecosystems. However, in a system with complex interacting components not all components provide the same quality of information to detect system-wide transitions. Identifying the best indicator species in complex ecosystems is a challenging task when a model of the system is not available. In this paper, we propose a data-driven approach to rank the elements of a spatially distributed ecosystem based on their reliability in providing early-warning signals of critical transitions. The proposed method is rooted in experimental modal analysis techniques traditionally used to identify structural dynamical systems. We show that one could use natural system fluctuations and the system responses to small perturbations to reveal the slowest direction of the system dynamics and identify indicator regions that are best suited for detecting abrupt transitions in a network of interacting components. The approach is applied to several ecosystems to demonstrate how it successfully ranks regions based on their reliability to provide early-warning signals of regime shifts. The significance of identifying the indicator species and the challenges associated with ranking nodes in networks of interacting components are also discussed.

Adsorption of a poorly water-soluble drug onto porous calcium silicate by the sealed heating method.

To improve the bioavailability of orally-administered drug, solubilization of poorly water-soluble drug is important. The solubility of a drug in its amorphous form is known to be higher than in its crystalline form. In this study, we attempted to adsorb a sublimable drug onto porous calcium silicate (Florite®, FLR) or non-porous calcium silicate (NPCS) by the sealed heating (SH) method and evaporated (EV) method. Ibuprofen (IBU) was used as the poorly water-soluble, sublimable drug. The physicochemical properties of samples were investigated using powder X-ray diffractometry (PXRD), differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FTIR), and dissolution test. From the PXRD and DSC results, IBU crystals were adsorbed and amorphized by the SH and EV methods with FLR. From the results of FTIR, the shift to a higher frequency by the carbonyl stretching vibration band of IBU suggests an intermolecular interaction between IBU and FLR. In SH with FLR, improved solubilization was observed. IBU adsorbed onto FLR showed a greater dissolution rate than the IBU crystals or NPCS. Thus, the petal-like structure of FLR may be an effective method to adsorb IBU onto FLR using the SH method.

Specific gut microbiome signature predicts the early-stage lung cancer.

Alterations of gut microbiota have been implicated in multiple diseases including cancer. However, the gut microbiota spectrum in lung cancer remains largely unknown. Here we profiled the gut microbiota composition in a discovery cohort containing 42 early-stage lung cancer patients and 65 healthy individuals through the 16S ribosomal RNA (rRNA) gene sequencing analysis. We found that lung cancer patients displayed a significant shift of microbiota composition in contrast to the healthy populations. To identify the optimal microbiota signature for noninvasive diagnosis purpose, we took advantage of Support-Vector Machine (SVM) and found that the predictive model with 13 operational taxonomic unit (OTU)-based biomarkers achieved a high accuracy in lung cancer prediction (area under curve, AUC = 97.6%). This signature performed reasonably well in the validation cohort (AUC = 76.4%), which contained 34 lung cancer patients and 40 healthy individuals. To facilitate potential clinical practice, we further constructed a 'patient discrimination index' (PDI), which largely retained the prediction efficiency in both the discovery cohort (AUC = 92.4%) and the validation cohort (AUC = 67.7%). Together, our study uncovered the microbiota spectrum of lung cancer patients and established the specific gut microbial signature for the potential prediction of the early-stage lung cancer.

[Application Value of Capillary Electrophoresis in Screeningß-Thalassemia of Children].

OBJECTIVE: to explore the value of capillary electrophoresis in screening ß- thalassemia of children, and to establish the cutoff values of HbA2 and HbF in our laboratory. METHODS: The data of hemoglobin capillary electrophoresis and genetic diagnosis of ß- thalassemia from 886 examined children were retrospectively analyzed. The cutoff values of HbA2 and HbF were determined by ROC curve. RESULTS: The cutoff value of HbA2 screening minor ß- thalassemia was 3.65%, the specificity was 0.996, and the sensitivity was 0.995. The cut-off value of HbF for screening minor ß- thalassemia was 1.45%, specificity was 0.751 and sensitivity was 0.675. Thus, 1 case with codon5 (CCT→C) mutation, 1 case with SEA -HPFH ß deletion, 1 case with - 28 (A→G) merger IVS-Ι-128 (T→G) double heterozygous mutations yet were found out, 1 case with 47 bp ß gene missing has not yet been reported in literature. CONCLUSION: Capillary electrophoresis has more high sensitivity and specificity in the screening of ß- thalassemia in children, especially for the detection of rare ß- thalassemia.