Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.

This article describes the Cell Maps for Artificial Intelligence (CM4AI) project and its goals, methods, standards, current datasets, software tools , status, and future directions. CM4AI is the Functional Genomics Data Generation Project in the U.S. National Institute of Health's (NIH) Bridge2AI program. Its overarching mission is to produce ethical, AI-ready datasets of cell architecture, inferred from multimodal data collected for human cell lines, to enable transformative biomedical AI research.

Regioisomerism in Thienothiophene-Based Covalent Organic Frameworks─A Tool for Band-Gap Engineering.

The craft of tuning optical properties is well-established for crystalline inorganic and hybrid solids. However, a far greater challenge is to tune the optical properties of organic materials systematically by design. We now introduce a synthesis concept that enables us to alter the optical properties of crystalline covalent organic frameworks (COFs) systematically using isomeric structures of thienothiophene-based building blocks (T23/32T) combined with a variety of tetratopic aromatic amines, e.g., the Wurster moiety (W-NH2). This concept is demonstrated for the synthesis of COFs in bulk and film forms and provides highly crystalline and porous isomeric COFs featuring predesigned photophysical properties. The band gap of the framework can be tuned continuously and precisely by chemically doping the pristine W23TT COF with its related constitutional isomer building block. Density-functional theory investigations of COF model compounds indicate that the extent of π-conjugation is among the key characteristics enabling the band-gap engineering.

Estimating maximum oxygen uptake of fishes during swimming and following exhaustive chase - different results, biological bases and applications.

The maximum rate at which animals take up oxygen from their environment (MO2,max) is a crucial aspect of their physiology and ecology. In fishes, MO2,max is commonly quantified by measuring oxygen uptake either during incremental swimming tests or during recovery from an exhaustive chase. In this Commentary, we compile recent studies that apply both techniques to the same fish and show that the two methods typically yield different mean estimates of MO2,max for a group of individuals. Furthermore, within a group of fish, estimates of MO2,max determined during swimming are poorly correlated with estimates determined during recovery from chasing (i.e. an individual's MO2,max is not repeatable across methods). One explanation for the lack of agreement is that these methods measure different physiological states, each with their own behavioural, anatomical and biochemical determinants. We propose that these methods are not directly interchangeable but, rather, each is suited to address different questions in fish biology. We suggest that researchers select the method that reflects the biological contexts of their study, and we advocate for the use of accurate terminology that acknowledges the technique used to elevate MO2 (e.g. peak MO2,swim or peak MO2,recovery). If the study's objective is to estimate the 'true' MO2,max of an individual or species, we recommend that pilot studies compare methods, preferably using repeated-measures designs. We hope that these recommendations contribute new insights into the causes and consequences of variation in MO2,max within and among fish species.

Controlling Interchromophore Coupling in Diamantane-Linked Pentacene Dimers To Create a "Binary" Pair.

Two isomeric pentacene dimers, each linked by a diamantane spacer, have been synthesized. These dimers are designed to provide experimental evidence to support quantum mechanical calculations, which predict the substitution pattern on the carbon-rich diethynyldiamantane spacer to be decisive in controlling the interpentacene coupling. Intramolecular singlet fission (i-SF) serves as a probe for the existence and strength of the electronic coupling between the two pentacenes, with transient absorption spectroscopy as the method of choice to characterize i-SF. 4,9-Substitution of diamantane provides a pentacene dimer (4,9-dimer) in which the two chromophores are completely decoupled and that, following photoexcitation, deactivates to the ground state analogous to a monomeric pentacene chromophore. Conversely, 1,6-substitution provides a pentacene dimer (1,6-dimer) that exhibits sufficiently strong coupling to drive i-SF, resulting in correlated triplet M(T1T1) yields close to unity and free triplet (T1 + T1) yields of ca. 50%. Thus, the diamantane spacer effectively switches "on" or "off" the coupling between the chromophores, based on the substitution pattern. The binary control of diamantane contrasts other known molecular spacers designed only to modulate the coupling strength between two pentacenes.

Determinants of Neutral Antagonism and Inverse Agonism in the ß2-Adrenergic Receptor.

Free-energy profiles for the activation/deactivation of the ß2-adrenergic receptor (ADRB2) with neutral antagonist and inverse agonist ligands have been determined with well-tempered multiple-walker (MW) metadynamics simulations. The inverse agonists carazolol and ICI118551 clearly favor single inactive conformational minima in both the binary and ternary ligand-receptor-G-protein complexes, in accord with the inverse-agonist activity of the ligands. The behavior of neutral antagonists is more complex, as they seem also to affect the recruitment of the G-protein. The results are analyzed in terms of the conformational states of the well-known microswitches that have been proposed as indicators of receptor activity.

Specific dynamic action: the energy cost of digestion or growth?

The physiological processes underlying the post-prandial rise in metabolic rate, most commonly known as the 'specific dynamic action' (SDA), remain debated and controversial. This Commentary examines the SDA response from two opposing hypotheses: (i) the classic interpretation, where the SDA represents the energy cost of digestion, versus (ii) the alternative view that much of the SDA represents the energy cost of growth. The traditional viewpoint implies that individuals with a reduced SDA should grow faster given the same caloric intake, but experimental evidence for this effect remains scarce and inconclusive. Alternatively, we suggest that the SDA reflects an organism's efficacy in allocating the ingested food to growth, emphasising the role of post-absorptive processes, particularly protein synthesis. Although both viewpoints recognise the trade-offs in energy allocation and the dynamic nature of energy distribution among physiological processes, we argue that equating the SDA with 'the energy cost of digestion' oversimplifies the complexities of energy use in relation to the SDA and growth. In many instances, a reduced SDA may reflect diminished nutrient absorption (e.g. due to lower digestive efficiency) rather than increased 'free' energy available for somatic growth. Considering these perspectives, we summarise evidence both for and against the opposing hypotheses with a focus on ectothermic vertebrates. We conclude by presenting a number of future directions for experiments that may clarify what the SDA is, and what it is not.

Percutaneous Management of Dialysis Access Steal Syndrome: Interventions and Outcomes from a Single Institution's 20-Year Experience.

PURPOSE: To determine safety and effectiveness of percutaneous interventions performed by interventional radiologists at a single institution over 2 decades in patients with dialysis access steal syndrome (DASS). MATERIALS AND METHODS: A retrospective review of fistulograms from 2001 to 2021 (N = 11,658) was performed. In total, 286 fistulograms in 212 patients with surgically created dialysis accesses met inclusion criterion of fistulography for suspected DASS. Chart review collected data regarding patient demographics, comorbidities, access characteristics, fistulography findings, intervention(s) performed, and outcomes. Procedures with and without DASS intervention were compared. Odds ratios (ORs), adjusted for age, sex, comorbidities, access characteristics, and multiple within-patient events, were calculated using logistic regression to determine associations between steal intervention status and outcome variables: (a) major adverse events, (b) access preservation, and (c) follow-up surgery. A percutaneously treatable cause of DASS was present in 128 cases (45%). Treatment of DASS lesions was performed in 118 cases. Fifteen embolizations were also performed in patients without DASS lesions. RESULTS: Technical success of DASS interventions, defined by the Society of Interventional Radiology (SIR) reporting standards, was 94%; 54% of interventions resulted in DASS symptom improvement at a median follow-up of 15 days. Patients with steal intervention had 60% lower odds of follow-up surgery (OR, 0.4; P = .007). There was no difference in major adverse events (P = .98) or access preservation (P = .13) between groups. CONCLUSIONS: In this retrospective cohort study, approximately half of DASS fistulograms revealed a percutaneously treatable cause of steal. Over half of DASS interventions resulted in symptomatic relief. Percutaneous intervention was associated with lower odds of follow-up surgery without compromising access preservation.

Radiofrequency guidewire-facilitated recanalization of chronic thoracic central venous occlusions in hemodialysis patients.

PURPOSE: To assess the outcome and safety of radiofrequency (RF) wire recanalization in patients with end-stage renal disease (ESRD) and chronic central venous occlusions (CVO). MATERIALS AND METHODS: A retrospective review of ESRD patients who underwent RF-wire recanalization of symptomatic chronic thoracic CVO from January 2017 to August 2022 yielded 20 patients who underwent 21 procedures. All patients had undergone at least one prior unsuccessful attempt at central venous recanalization using conventional catheter-based techniques. Technical success was defined by the ability to cross the CVO using RF-wire recanalization enabling endovascular treatment. Access circuit patency was evaluated based on follow-up imaging and symptomatic improvement. RESULTS: Radiofrequency wire recanalization was successful in 17/21 procedures (81%) with all patients (100%) reporting resolution of arm ± facial swelling. Three major complications occurred (14%): two hemothoraces and one hemopericardium. Medial stent diameter was 13 mm (range, 9-14 mm). Mean duration of hospital stay was 2 days ± 3 days. Mean procedure time was 158 ± 46 min with a mean fluoroscopy time of 31.7 ± 16.3 min. Primary unassisted patency at 6 and 12 months was 94 ± 6% and 85 ± 10%, respectively. Additional interventions resulted in significantly increased stent graft patency (P = 0.006). CONCLUSION: Radiofrequency wire-enabled recanalization of CVO in symptomatic dialysis patients has a high rate of technical success with resolution of arm and facial swelling and resumed use of the ipsilateral dialysis access. Although a superior safety profile was seen than with needle-based techniques such as sharp recanalization, major complications were not infrequent indicating that this RF-wire procedure should be performed in centers equipped to manage central venous perforations.

Association between End-Stage Renal Disease and Major Adverse Limb Events after Peripheral Vascular Intervention.

PURPOSE: To examine the effect of end-stage renal disease (ESRD) on the likelihood of major adverse limb events (MALEs) in patients with Rutherford Category 4-6 critical limb ischemia (CLI) who underwent percutaneous vascular intervention (PVI). MATERIALS AND METHODS: Two contemporaneous cohorts of patients who underwent PVI for symptomatic CLI from 2012 to 2022, differing in ESRD status, were matched using propensity score methods. This database identified 628 patients who underwent 1,297 lower extremity revascularization procedures; propensity score matching yielded 147 patients (180 limbs, 90 limbs in each group). Kaplan-Meier and Cox proportional hazard analyses were used to assess the effect of ESRD status on MALEs, stratified into major amputation (further stratified into above-knee amputation and below-knee amputation [BKA]) and reintervention (PVI or bypass). RESULTS: After PVI, 31.3% of patients in the matched cohorts experienced a MALE (45.7% ESRD vs 18.2% non-ESRD), and 15.6% experienced a major amputation (27.1% ESRD vs 5.2% non-ESRD). Cox proportional hazards analysis revealed that ESRD was an independent predictor of MALE (hazard ratio [HR], 3.15; 95% CI, 1.58-6.29; P = .001), major amputation (HR, 7.00; 95% CI, 2.06-23.79; P = .002), and BKA (HR, 7.56; 95% CI, 1.71-33.50; P = .008). CONCLUSIONS: ESRD is strongly predictive of MALE and major amputation risk, specifically BKA, in patients undergoing PVI for Rutherford Category 4-6 CLI. These patients warrant closer follow-up, and new methods may become necessary to predict and further reduce their amputation risk.

Intramolecular Triplet Diffusion Facilitates Triplet Dissociation in a Pentacene Hexamer.

Triplet dynamics in singlet fission depend strongly on the strength of the electronic coupling. Covalent systems in solution offer precise control over such couplings. Nonetheless, efficient free triplet generation remains elusive in most systems, as the intermediate triplet pair 1 (T1 T1 ) is prone to triplet-triplet annihilation due to its spatial confinement. In the solid state, entropically driven triplet diffusion assists in the spatial separation of triplets, resulting in higher yields of free triplets. Control over electronic coupling in the solid state is, however, challenging given its sensitivity to molecular packing. We have thus developed a hexameric system (HexPnc) to enable solid-state-like triplet diffusion at the molecular scale. This system is realized by covalently tethering three pentacene dimers to a central subphthalocyanine scaffold. Transient absorption spectroscopy, complemented by theoretical structural optimizations and steady-state spectroscopy, reveals that triplet diffusion is indeed facilitated due to intramolecular cluster formation. The yield of free triplets in HexPnc is increased by a factor of up to 14 compared to the corresponding dimeric reference (DiPnc). Thus, HexPnc establishes crucial design aspects for achieving efficient triplet dissociation in strongly coupled systems by providing avenues for diffusive separation of 1 (T1 T1 ), while, concomitantly, retaining strong interchromophore coupling which preserves rapid formation of 1 (T1 T1 ).

Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors.

A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.

Supplemental oxygen does not improve growth but can enhance reproductive capacity of fish.

Fish tend to grow faster as the climate warms but attain a smaller adult body size following an earlier age at sexual maturation. Despite the apparent ubiquity of this phenomenon, termed the temperature-size rule (TSR), heated scientific debates have revealed a poor understanding of the underlying mechanisms. At the centre of these debates are prominent but marginally tested hypotheses which implicate some form of 'oxygen limitation' as the proximate cause. Here, we test the role of oxygen limitation in the TSR by rearing juvenile Galaxias maculatus for a full year in current-day (15°C) and forecasted (20°C) summer temperatures while providing half of each temperature group with supplemental oxygen (hyperoxia). True to the TSR, fish in the warm treatments grew faster and reached sexual maturation earlier than their cooler conspecifics. Yet, despite supplemental oxygen significantly increasing maximum oxygen uptake rate, our findings contradict leading hypotheses by showing that the average size at sexual maturation and the adult body size did not differ between normoxia and hyperoxia groups. We did, however, discover that hyperoxia extended the reproductive window, independent of fish size and temperature. We conclude that the intense resource investment in reproduction could expose a bottleneck where oxygen becomes a limiting factor.

Stereochemical Stability of Planar-Chiral Benzazepine Tricyclics: Inversion Energies of P- and S-Alkene Ligands.

Inversion barriers ΔG‡ for planar chiral phosphine-alkene and sulfonamide-alkene hybrid ligands based on phenyl-dibenz[b,f]azepine have been determined by density-functional theory calculations. Analysis of the structural and electronic characteristics of the minima and transition states explains the magnitudes of ΔG‡ and the geometrical changes during the inversion process. The steric repulsion caused by bulky substituents attached to the azepine nitrogen atom has a pronounced effect on the ΔG‡ value, explaining, inter alia, the stereochemical stability of the P- and S-alkene ligands when compared to the fluxional parent compound where X = H.

Driving the quadricyclane-to-norbornadiene isomerization by charge separation with perylenediimide as electron acceptor.

Through comprehensive photo-assays, this study investigates the reaction coordinate governing the interconversion between quadricyclane (QC) and norbornadiene (NBD) upon photo-irradiation up to a wavelength of 550 nm. To harness this spectroscopic range for energy release, we link the NBD-core with a highly electron-accepting perylenediimide (PDI) with broad absorption, achieving strong electronic coupling between them. We detail the successful synthesis and present extensive DFT calculations to determine the amount of stored energy. By means of transient absorption spectroscopy, an oxidative electron transfer is observed during the QC-to-NBD isomerization following the initial PDI photoexcitation. This charge-separated state is key to triggering the back-isomerization with visible light excitation.

Activation/Deactivation Free-Energy Profiles for the ß2-Adrenergic Receptor: Ligand Modes of Action.

We use enhanced-sampling simulations with an effective collective variable to study the activation of the ß2-adrenergic receptor in the presence of ligands with different efficacy. The free-energy profiles are computed for the ligand-free (apo) receptor and binary (apo-receptor + G-protein α-subunit and receptor + ligand) and ternary complexes. The results are not only compatible with available experiments but also allow unprecedented structural insight into the nature of GPCR conformations along the activation pathway and their role in the activation mechanism. In particular, the simulations reveal an unexpected mode of action of partial agonists such as salmeterol and salbutamol that arises already in the binary complex without the G-protein. Specific differences in the polar interactions with residues in TM5, which are required to stabilize an optimal TM6 conformation that facilitates G-protein binding and receptor activation, play a major role in differentiating them from full agonists.

Tetracene Dimers: A Platform for Intramolecular Down- and Up-conversion.

Photon energy conversion can be accomplished in many different ways, including the two opposing manners, down-conversion (i.e., singlet fission, SF) and up-conversion (i.e., triplet-triplet annihilation up-conversion, TTA-UC). Both processes have the potential to help overcome the detailed balance limit of single-junction solar cells. Tetracene, in which the energies of the lowest singlet excited state and twice the triplet excited state are comparable, exhibits both down- and up-conversion. Here, we have designed meta-diethynylphenylene- and 1,3-diethynyladamantyl-linked tetracene dimers, which feature different electronic coupling, to characterize the interplay between intramolecular SF (intra-SF) and intramolecular TTA-UC (intra-TTA-UC) via steady-state and time-resolved absorption and fluorescence spectroscopy. Furthermore, we have used Pd-phthalocyanine as a sensitizer to enable intra-TTA-UC in the two dimers via indirect photoexcitation in the near-infrared part of the solar spectrum. The work is rounded off by temperature-dependent measurements, which outline key aspects of how thermal effects impact intra-SF and intra-TTA-UC in different dimers.

Stereochemistry-Driven Interactions of α,γ-Peptide Ligands with the Neuropeptide Y Y4-Receptor.

The G-protein-coupled Y4-receptor (Y4R) and its endogenous ligand, pancreatic polypeptide (PP), suppress appetite in response to food intake and, thus, are attractive drug targets for body-weight control. The C-terminus of human PP (hPP), T32-R33-P34-R35-Y36-NH2, penetrates deep into the binding pocket with its tyrosine-amide and di-arginine motif. Here, we present two C-terminally amidated α,γ-hexapeptides (1a/b) with sequence Ac-R31-γ-CBAA32-R33-L34-R35-Y36-NH2, where γ-CBAA is the (1R,2S,3R)-configured 2-(aminomethyl)-3-phenylcyclobutanecarboxyl moiety (1a) or its mirror image (1b). Both peptides bind the Y4R (Ki of 1a/b: 0.66/12 nM) and act as partial agonists (intrinsic activity of 1a/b: 50/39%). Their induced-fit binding poses in the Y4R pocket are unique and build ligand-receptor contacts distinct from those of the C-terminus of the endogenous ligand hPP. We conclude that energetically favorable interactions, although they do not match those of the native ligand hPP, still guarantee high binding affinity (with 1a rivaling hPP) but not the maximum receptor activation.

Evidence for energy reallocation, not oxygen limitation, driving the deceleration in growth of adult fish.

The lifetime growth of almost all fishes follows a biphasic relationship - juvenile growth is rapid and adult growth subsequently decelerates. For a trend that is so ubiquitous, there is no general agreement as to the underlying mechanisms causing adult growth to decelerate. Ongoing theories argue that adult growth slows because either the gills fail to supply the body with surplus oxygen needed for continued somatic gain (i.e. oxygen limited), or sexual maturation induces a switch in energy allocation towards reproduction and away from growth (i.e. energy limited). Here, we empirically tested these notions by tracking the individual growth trajectories of ∼100 female Galaxias maculatus, ranging in size, during their first 3 months of adulthood. At a summer temperature of 20°C, we provided subsets of fish with additional energy (fed once versus twice a day), supplementary oxygen (normoxia versus hyperoxia), or a combination of the two, to assess whether we could change the trajectory of adult growth. We found that growth improved marginally with additional energy, yet remained unaffected by supplementary oxygen, thereby providing evidence for a role for energy reallocation in the deceleration of adult growth. Interestingly, additional dietary energy had a disproportionately larger effect on the growth of fish that matured at a greater size, revealing size-dependent variance in energy acquisition and/or allocation budgets at summer temperatures. Overall, these findings contribute towards understanding the mechanisms driving widespread declines in the body size of fish with climate warming.