PViT-AIR: Puzzling vision transformer-based affine image registration for multi histopathology and faxitron images of breast tissue.

Breast cancer is a significant global public health concern, with various treatment options available based on tumor characteristics. Pathological examination of excision specimens after surgery provides essential information for treatment decisions. However, the manual selection of representative sections for histological examination is laborious and subjective, leading to potential sampling errors and variability, especially in carcinomas that have been previously treated with chemotherapy. Furthermore, the accurate identification of residual tumors presents significant challenges, emphasizing the need for systematic or assisted methods to address this issue. In order to enable the development of deep-learning algorithms for automated cancer detection on radiology images, it is crucial to perform radiology-pathology registration, which ensures the generation of accurately labeled ground truth data. The alignment of radiology and histopathology images plays a critical role in establishing reliable cancer labels for training deep-learning algorithms on radiology images. However, aligning these images is challenging due to their content and resolution differences, tissue deformation, artifacts, and imprecise correspondence. We present a novel deep learning-based pipeline for the affine registration of faxitron images, the x-ray representations of macrosections of ex-vivo breast tissue, and their corresponding histopathology images of tissue segments. The proposed model combines convolutional neural networks and vision transformers, allowing it to effectively capture both local and global information from the entire tissue macrosection as well as its segments. This integrated approach enables simultaneous registration and stitching of image segments, facilitating segment-to-macrosection registration through a puzzling-based mechanism. To address the limitations of multi-modal ground truth data, we tackle the problem by training the model using synthetic mono-modal data in a weakly supervised manner. The trained model demonstrated successful performance in multi-modal registration, yielding registration results with an average landmark error of 1.51 mm (±2.40), and stitching distance of 1.15 mm (±0.94). The results indicate that the model performs significantly better than existing baselines, including both deep learning-based and iterative models, and it is also approximately 200 times faster than the iterative approach. This work bridges the gap in the current research and clinical workflow and has the potential to improve efficiency and accuracy in breast cancer evaluation and streamline pathology workflow.

In Silico Evaluation and Experimental Validation of Interfacial Properties in 3-5 Residue Peptides.

Predicting the interfacial properties of peptides is important for replacing oil-derived surfactants in cosmetics, oil, and agricultural applications. This work validated experimentally the estimations of surface tension at the critical micelle concentration (STCMC) of six peptides performed through a random forest (RF) model in a previous contribution. In silico interfacial tensions of the peptides were obtained in the system decane-water, and dilational experiments were applied to elucidate the foaming potential. The RF model accurately classified the peptides into high and low potential to reduce the STCMC. The simulations at the decane-water interface correctly identified peptides with high, intermediate, and low interfacial properties, and the dilational rheology allowed the estimation of the possible potential of three peptides to produce foams. This study sets the basis for identifying surface-active peptides, but future work is necessary to improve the estimations and the correlation between dilational properties and foam stabilization.

TMCO1 is upregulated in breast cancer and regulates the response to pro-apoptotic agents in breast cancer cells.

The release of Ca2+ ions from endoplasmic reticulum calcium stores is a key event in a variety of cellular processes, including gene transcription, migration and proliferation. This release of Ca2+ often occurs through inositol 1,4,5-triphosphate receptors and the activity of these channels and the levels of stored Ca2+ in the endoplasmic reticulum are important regulators of cell death in cancer cells. A recently identified Ca2+ channel of the endoplasmic reticulum is transmembrane and coiled-coil domains 1 (TMCO1). In this study, we link the overexpression of TMCO1 with prognosis in node-positive basal breast cancer patients. We also identify interacting proteins of TMCO1, which include endoplasmic reticulum-resident proteins involved in Ca2+ regulation and proteins directly involved in nucleocytoplasmic transport. Interacting proteins included nuclear transport proteins and TMCO1 was shown to have both nuclear and endoplasmic reticulum localisation in MDA-MB-231 basal breast cancer cells. These studies also define a role for TMCO1 in the regulation of breast cancer cells in their sensitivity to BCL-2/MCL-1 inhibitors, analogous to the role of inositol 1,4,5-triphosphate receptors in the regulation of cell death pathways activated by these agents.

Interactions between prosulfocarb and trifluralin metabolism in annual ryegrass (Lolium rigidum).

BACKGROUND: Cross-resistance between pre-emergence herbicides is developing in Australian populations of annual ryegrass (Lolium rigidum Gaud.). A previous study has reported that selection with prosulfocarb (a pro-herbicide requiring bioactivation to its phytotoxic sulfoxide) can decrease metabolic resistance to trifluralin. Metabolism of prosulfocarb and trifluralin was investigated in L. rigidum populations with different levels of resistance to prosulfocarb, trifluralin and also pyroxasulfone, which is detoxified by glutathione (GSH) conjugation. RESULTS: Coleoptiles and radicles of herbicide-treated seedlings responded differently to the same herbicide. Radicles had a lower capacity for bioactivation of prosulfocarb, and this was correlated with a lower ability to metabolise trifluralin within and among populations. Coleoptile resistance to prosulfocarb sulfoxide was negatively correlated with abundance of a major polar metabolite. There was no evidence of GSH conjugation with the sulfoxide, making any potential links between prosulfocarb and pyroxasulfone resistance less obvious. CONCLUSIONS: Activation and metabolism of prosulfocarb in L. rigidum is complex and differentially regulated in different tissues. Selection with prosulfocarb may ameliorate trifluralin metabolism in the radicles, but the relationship between prosulfocarb and pyroxasulfone resistance is not GSH-mediated. When applying pre-emergence herbicides, care should be taken with the composition of mixtures and rotations to avoid selection of cross-resistance between pyroxasulfone and prosulfocarb. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Reexploring the conception of heat-health risk: From the perspectives of dimensionality and spatiality.

Extreme heat events are more frequent and intense as a result of global climate change, thus posing tremendous threats to public health. However, extant literature exploring the multidimensional features of heat-health risks from a spatial perspective is limited. This study revisits extreme heat-health risk and decomposes this concept by integrating multi-sourced datasets, identifying compositional features, examining spatial patterns, and comparing classified characteristics based on local conditions. Using Maryland as the focal point, we found that the components of heat-health risk are different from traditional risk dimensions (i.e., vulnerability, hazards, and exposure). Through a local-level clustering analysis, heat-health risks were compared with areas having similar features, and among those with different features. The findings suggest a new perspective for understanding the socio-environmental and socio-spatial features of heat-health risks. They also offer an apt example of applying cross-disciplinary methods and tools for investigating an ever-changing phenomenon. Moreover, the spatial classification mechanism provides insights about the underlying causes of heat-health risk disparities and offers reference points for decision-makers regarding identification of vulnerable areas, resource allocation, and causal inferences when planning for and managing extreme heat disasters.

Expanding the inhibitor space of the WWP1 and WWP2 HECT E3 ligases.

The HECT E3 ubiquitin ligases 1 (WWP1) and 2 (WWP2) are responsible for the ubiquitin-mediated degradation of key tumour suppressor proteins and are dysregulated in various cancers and diseases. Here we expand their limited inhibitor space by identification of NSC-217913 displaying a WWP1 IC50 of 158.3 µM (95% CI = 128.7, 195.1 µM). A structure-activity relationship by synthesis approach aided by molecular docking led to compound 11 which displayed increased potency with an IC50 of 32.7 µM (95% CI = 24.6, 44.3 µM) for WWP1 and 269.2 µM (95% CI = 209.4, 347.9 µM) for WWP2. Molecular docking yielded active site-bound poses suggesting that the heterocyclic imidazo[4,5-b]pyrazine scaffold undertakes a π-stacking interaction with the phenolic group of tyrosine, and the ethyl ester enables strong ion-dipole interactions. Given the therapeutic potential of WWP1 and WWP2, we propose that compound 11 may provide a basis for future lead compound development.

The "Doorstop Pocket" In Thioredoxin Reductases─An Unexpected Druggable Regulator of the Catalytic Machinery.

Pyridine nucleotide-disulfide oxidoreductases are underexplored as drug targets, and thioredoxin reductases (TrxRs) stand out as compelling pharmacological targets. Selective TrxR inhibition is challenging primarily due to the reliance on covalent inhibition strategies. Recent studies identified a regulatory and druggable pocket in Schistosoma mansoni thioredoxin glutathione reductase (TGR), a TrxR-like enzyme, and an established drug target for schistosomiasis. This site is termed the "doorstop pocket" because compounds that bind there impede the movement of an aromatic side-chain necessary for the entry and exit of NADPH and NADP+ during enzymatic turnover. This discovery spearheaded the development of new TGR inhibitors with efficacies surpassing those of current schistosomiasis treatment. Targeting the "doorstop pocket" is a promising strategy, as the pocket is present in all members of the pyridine nucleotide-disulfide oxidoreductase family, opening new avenues for exploring therapeutic approaches in diseases where the importance of these enzymes is established, including cancer and inflammatory and infectious diseases.

Localized delivery of therapeutics impact laryngeal mechanics, local inflammatory response, and respiratory microbiome following upper airway intubation injury in swine.

BACKGROUND: Laryngeal injury associated with traumatic or prolonged intubation may lead to voice, swallow, and airway complications. The interplay between inflammation and microbial population shifts induced by intubation may relate to clinical outcomes. The objective of this study was to investigate laryngeal mechanics, tissue inflammatory response, and local microbiome changes with laryngotracheal injury and localized delivery of therapeutics via drug-eluting endotracheal tube. METHODS: A simulated traumatic intubation injury was created in Yorkshire crossbreed swine under direct laryngoscopy. Endotracheal tubes electrospun with roxadustat or valacyclovir- loaded polycaprolactone (PCL) fibers were placed in the injured airway for 3, 7, or 14 days (n = 3 per group/time and ETT type). Vocal fold stiffness was then evaluated with normal indentation and laryngeal tissue sections were histologically examined. Immunohistochemistry and inflammatory marker profiling were conducted to evaluate the inflammatory response associated with injury and ETT placement. Additionally, ETT biofilm formation was visualized using scanning electron microscopy and micro-computed tomography, while changes in the airway microbiome were profiled through 16S rRNA sequencing. RESULTS: Laryngeal tissue with roxadustat ETT placement had increasing localized stiffness outcomes over time and histological assessment indicated minimal epithelial ulceration and fibrosis, while inflammation remained severe across all timepoints. In contrast, vocal fold tissue with valacyclovir ETT placement showed no significant changes in stiffness over time; histological analysis presented a reduction in epithelial ulceration and inflammation scores along with increased fibrosis observed at 14 days. Immunohistochemistry revealed a decline in M1 and M2 macrophage markers over time for both ETT types. Among the cytokines, IL-8 levels differed significantly between the roxadustat and valacyclovir ETT groups, while no other cytokines showed statistically significant differences. Additionally, increased biofilm formation was observed in the coated ETTs with notable alterations in microbiota distinctive to each ETT type and across time. CONCLUSION: The injured and intubated airway resulted in increased laryngeal stiffness. Local inflammation and the type of therapeutic administered impacted the bacterial composition within the upper respiratory microbiome, which in turn mediated local tissue healing and recovery.

A moving target: trade-offs between maximizing carbon and minimizing hydraulic stress for plants in a changing climate.

Observational evidence indicates that tree leaf area may acclimate in response to changes in water availability to alleviate hydraulic stress. However, the underlying mechanisms driving leaf area changes and consequences of different leaf area allocation strategies remain unknown. Here, we use a trait-based hydraulically enabled tree model with two endmember leaf area allocation strategies, aimed at either maximizing carbon gain or moderating hydraulic stress. We examined the impacts of these strategies on future plant stress and productivity. Allocating leaf area to maximize carbon gain increased productivity with high CO2, but systematically increased hydraulic stress. Following an allocation strategy to avoid increased future hydraulic stress missed out on 26% of the potential future net primary productivity in some geographies. Both endmember leaf area allocation strategies resulted in leaf area decreases under future climate scenarios, contrary to Earth system model (ESM) predictions. Leaf area acclimation to avoid increased hydraulic stress (and potentially the risk of accelerated mortality) was possible, but led to reduced carbon gain. Accounting for plant hydraulic effects on canopy acclimation in ESMs could limit or reverse current projections of future increases in leaf area, with consequences for the carbon and water cycles, and surface energy budgets.

The probability of cryptic pocket opening controls functional tradeoffs in filovirus immune evasion.

Cryptic pockets are of growing interest as potential drug targets. However, it remains unclear whether they contribute to protein function or if they are merely happenstantial features that can easily be evolved away to achieve drug resistance. Here, we explore whether a cryptic pocket in the Interferon Inhibitory Domain (IID) of viral protein 35 (VP35) of Zaire ebolavirus has a functional role. We use simulations and experiments to study the relationship between cryptic pocket opening and double-stranded RNA (dsRNA) binding of the IIDs of two other filoviruses, Reston and Marburg. These homologs have structures nearly identical to Zaire but block different interferon pathways because Marburg IID only binds the backbone, while Zaire and Reston IIDs bind both backbone and blunt ends of dsRNA. We hypothesized that these differences arise from alterations in their pocket dynamics. Simulations and thiol-labeling experiments demonstrate that Reston has a lower probability of opening the cryptic pocket while Marburg has a higher probability than Zaire. Subsequent dsRNA-binding assays with different length substrates suggest that closed conformations preferentially bind dsRNA blunt ends while open conformations prefer binding the backbone. Further, a point mutation that increases the probability of cryptic pocket opening in Reston shows that the open states prefer backbone binding, while a substitution that lowers the probability of pocket opening in Zaire improves binding to blunt ends. These results demonstrate the cryptic pocket controls a functional tradeoff, suggesting cryptic pockets are under selective pressure and may be difficult to evolve away to achieve drug resistance.

Suppression of neuronal AMPKß2 isoform impairs recognition memory and synaptic plasticity.

AMP-activated protein kinase (AMPK) is an αßγ heterotrimer protein kinase that functions as a molecular sensor to maintain energy homeostasis. Accumulating evidence suggests a role of AMPK signaling in the regulation of synaptic plasticity and cognitive function; however, isoform-specific roles of AMPK in the central nervous system (CNS) remain elusive. Regulation of the AMPK activities has focused on the manipulation of the α or γ subunit. Meanwhile, accumulating evidence indicates that the ß subunit is critical for sensing nutrients such as fatty acids and glycogen to control AMPK activity. Here, we generated transgenic mice with conditional suppression of either AMPKß1 or ß2 in neurons and characterized potential isoform-specific roles of AMPKß in cognitive function and underlying mechanisms. We found that AMPKß2 (but not ß1) suppression resulted in impaired recognition memory, reduced hippocampal synaptic plasticity, and altered structure of hippocampal postsynaptic densities and dendritic spines. Our study implicates a role for the AMPKß2 isoform in the regulation of synaptic and cognitive function.

Synthesis and in vitro evaluation shows disquaramide compounds are a promising class of anti-leishmanial drugs.

An increasing number of treatment failures with current pharmaceutics, as well as a lack of a vaccine, demonstrates the need to develop new treatment options for leishmaniasis. Herein, we describe the synthesis and in vitro analysis of 24 disquaramide compounds targeting the Leishmania major parasite. Of the compounds that were evaluated, six of them ( 13 , 19 , 20 , 22 , 24 , and 26 ) were capable of significantly decreasing the number of parasites by up to 42% compared to the control by day four. This demonstrates that disquaramides either impair parasite replication or have leishmancidal effects. Additionally, none of the disquaramide compounds tested displayed host cell cytotoxicity. These experiments provide evidence that disquaramides have the potential to be effective anti-leishmanial therapeutics.

Self-sensitized photodegradation and adsorption of aqueous malachite green dye using one-dimensional titanium oxide nanofilaments.

Truly one-dimensional titanium oxide nanofilaments with a lepidocrocite structure (1DLs) were explored in the adsorption and photocatalytic degradation of aqueous malachite green (MG), a toxic polluting dye. Decolorization is monitored by ultraviolet-visible spectroscopy, and mineralization is confirmed by total organic carbon analysis. The 1DL/MG flocs are characterized by scanning electron microscopy and X-ray diffraction. 1DLs, a colloidal nanomaterial, exhibit flocculating behavior while demonstrating high affinity for MG, with a maximum uptake of >680 mg/g rapidly via ion exchange. Additionally, 1DLs decolorize MG under visible light only, unlike most available titania products, via a self-sensitization effect. MG is decolorized by 1DLs by >70% in 30 min under 1 sun exposure of visible light. Counterintuitively, dye adsorption increases as the normalized concentration by mass of 1DL decreases. Demonstrating high adsorption capacity and dye mineralization supports the use of 1DLs in water treatment and self-sensitization for photoelectrochemical devices, like solar cells.

VISION: An Individual Patient Data Meta-analysis of Randomised Trials Comparing Magnetic Resonance Imaging Targeted Biopsy with Standard Transrectal Ultrasound Guided Biopsy in the Detection of Prostate Cancer.

BACKGROUND AND OBJECTIVE: The PRECISION and PRECISE trials compared magnetic resonance imaging targeted biopsy (MRI ± TB) with the standard transrectal ultrasound (TRUS) guided biopsy for the detection of clinically significant prostate cancer (csPCa). PRECISION demonstrated superiority of MRI ± TB over TRUS guided biopsy, while PRECISE demonstrated noninferiority. The VISION study is a planned individual patient data meta-analysis (IPDMA) comparing MRI ± TB with TRUS guided biopsy for csPCa diagnosis. METHODS: MEDLINE, EMBASE, Web of Science, Cochrane Central of Registered Trials, and ClinicalTrials.gov were searched on the November 12, 2023 for randomised controlled trials of biopsy-naïve patients with a clinical suspicion of prostate cancer undergoing MRI or standard TRUS. Studies were included if its participants with suspicious MRI underwent targeted biopsy alone and those with nonsuspicious lesion avoided biopsy. The primary outcome is the proportion of men diagnosed with csPCa (Gleason ≥3 + 4). KEY FINDINGS AND LIMITATIONS: Two studies, PRECISION and PRECISE (953 patients), were included in the IPDMA. In the MRI ± TB arm, 32.2% of patients avoided biopsy due to nonsuspicious MRI. MRI ± TB detected 8.7 percentage points (36.3% vs 27.6%; 95% confidence interval [CI] 2.8-14.6, p = 0.004) more csPCa than TRUS biopsy and 12.3 percentage points (9.6% vs 21.9%; 95% CI 7.8-16.9, p < 0.001) less clinically insignificant prostate cancer (cisPCa; Gleason 3 + 3). The overall risk of bias for the included studies were found to be low after assessment using the QUADAS-2, QUADAS-C, and ROB 2.0 tools. CONCLUSIONS AND CLINICAL IMPLICATIONS: The MRI ± TB pathway is superior to TRUS biopsy in detecting csPCa and avoiding the diagnosis of cisPCa. MRI should be included in the standard of care pathway for prostate cancer diagnosis.

Preserved memory for decisions across adulthood.

Remembering our decisions is crucial - it allows us to learn from past mistakes and construct future behavior. However, it is unclear if age-related memory declines impact the memorability of older adults' decisions. Here, we compared younger and older adults' ability to remember their decisions. In Studies 1 and 2, participants made choices between two objects based on their star rating (shopping context) or circle count (neutral context) and later remembered what they chose. while Study 3 tested participants' memory for active vs. passive decisions. Overall, we found no evidence for age differences in the ability to remember decisions. Furthermore, age did not interact with context - both similarly benefitted from making and remembering their decisions in a more shopping-like context. These results reveal an aspect of cognition that appears to be preserved in healthy aging. Highlighting such aspects can help improve older adults' self-perceptions and reframe the narrative around aging.

Characterization of the Vertical Stiffness Gradient in Cadaveric Human and Excised Canine Larynges.

The elastic properties of the folds govern the characteristics of vocal fold vibrations. This study addresses existing gaps by investigating the Young's modulus along the anterior-posterior direction in excised canine and cadaveric human vocal folds. Micro-indentation testing was conducted on six excised canines and three cadaveric human larynges. Multiple points along the medial glottal wall were indented to determine force-displacement, stress-strain relationships, and Young's modulus as a function of Green's strain. A vertical stiffness gradient was consistently observed in both canine and human samples, with higher stiffness in the inferior aspect compared with the superior aspect. The stiffness increased toward both the anterior and posterior directions from the mid-coronal plane, with a more pronounced increase at the posterior edge. Human vocal folds generally exhibited lower stiffness at low strains but were comparable to canine vocal folds at higher strains. These findings suggest that the canine larynx model is a reasonable representation of the human laryngeal tissues' elastic property trends. This analysis of the vertical stiffness gradient in canine and human vocal folds provides valuable data for improving experimental and numerical models of phonation.

Stabilization of interdomain closure by a G protein inhibitor.

Inhibitors of heterotrimeric G proteins are being developed as therapeutic agents. Epitomizing this approach are YM-254890 (YM) and FR900359 (FR), which are efficacious in models of thrombosis, hypertension, obesity, asthma, uveal melanoma, and pain, and under investigation as an FR-antibody conjugate in uveal melanoma clinical trials. YM/FR inhibits the Gq/11/14 subfamily by interfering with GDP (guanosine diphosphate) release, but by an unknown biophysical mechanism. Here, we show that YM inhibits GDP release by stabilizing closure between the Ras-like and α-helical domains of a Gα subunit. Nucleotide-free Gα adopts an ensemble of open and closed configurations, as indicated by single-molecule Förster resonance energy transfer and molecular dynamics simulations, whereas GDP and GTPγS (guanosine 5'-O-[gamma-thio]triphosphate) stabilize distinct closed configurations. YM stabilizes closure in the presence or absence of GDP without requiring an intact interdomain interface. All three classes of mammalian Gα subunits that are insensitive to YM/FR possess homologous but degenerate YM/FR binding sites, yet can be inhibited upon transplantation of the YM/FR binding site of Gq. Novel YM/FR analogs tailored to each class of G protein will provide powerful new tools for therapeutic investigation.

Targeted DNA Sequencing in Diagnosis of Malignant Phyllodes Tumors With Emphasis on Tumors With Keratin and p63 Expression.

The differential diagnosis of malignant spindle cell neoplasms in the breast most frequently rests between malignant phyllodes tumor (MPT) and metaplastic carcinoma (MBC). Diagnosis of MPT can be challenging due to diffuse stromal overgrowth, keratin (CK) and/or p63 immunopositivity, and absent CD34 expression, which can mimic MBC, especially in core biopsies. Distinction of MPT from MBC has clinical implications, with differences in surgical approach, chemotherapy, and radiation. In this study, we evaluated MPTs (78 tumors, 64 patients) for stromal CK, p63, and CD34 expression and profiled a subset (n = 31) by targeted next-generation DNA sequencing, with comparison to MBC (n = 44). Most MPTs (71%) were CK+ and/or p63+, including 32% CK+ (25/77 focal) and 65% p63+ (32/66 focal, 10/66 patchy, and 1/66 diffuse). Thirty percent of MPTs expressed both CK and p63 (20/66), compared with 95% of MBCs (40/42, P < .001). CK and/or p63 were positive in CD34+ and CD34- MPTs. Recurrent genetic aberrations in MPTs involved TERT, TP53, MED12, CDKN2A, chromatin modifiers, growth factor receptors/ligands, and phosphoinositide-3 kinase (PI-3K) and MAPK pathway genes. Only MED12 (39%, 12/31) and SETD2 (13%, 4/31) were exclusively mutated in MPTs and not MBCs (P < .001 and P = .044, respectively), whereas PIK3R1 mutations were only found in MBCs (37%, 13/35, P < .001). Comparative literature review additionally identified ARID1B, EGFR, FLNA, NRAS, PDGFRB, RAD50, and RARA alterations enriched or exclusively in MPTs vs MBCs. MED12 was mutated in MPTs with diffuse stromal overgrowth (53%, 9/17), CD34- MPTs (41%, 7/17), and CK+ and/or p63+ MPTs (39%, 9/23), including 36% of CD34- MPTs with CK and/or p63 expression. Overall, MED12 mutation and/or CD34 expression were observed in 68% (21/31) MPTs, including 61% (14/23) of CK+ and/or p63+ tumors. Our results emphasize the prevalence of CK and p63 expression in MPTs and demonstrate the diagnostic utility of next-generation DNA sequencing, especially in MPTs with confounding factors that can mimic MBC.