Mathematical models of coagulation-are we there yet?

BACKGROUND: Mathematical models of coagulation have been developed to mirror thrombin generation in plasma, with the aim of investigating how variation in coagulation factor levels regulates hemostasis. However, current models vary in the reactions they capture and the reaction rates used, and their validation is restricted by a lack of large coherent datasets, resulting in questioning of their utility. OBJECTIVES: To address this debate, we systematically assessed current models against a large dataset, using plasma coagulation factor levels from 348 individuals with normal hemostasis to identify the causes of these variations. METHODS: We compared model predictions with measured thrombin generation, quantifying and comparing the ability of each model to predict thrombin generation, the contributions of the individual reactions, and their dependence on reaction rates. RESULTS: We found that no current model predicted the hemostatic response across the whole cohort and all produced thrombin generation curves that did not resemble those obtained experimentally. Our analysis has identified the key reactions that lead to differential model predictions, where experimental uncertainty leads to variability in predictions, and we determined reactions that have a high influence on measured thrombin generation, such as the contribution of factor XI. CONCLUSION: This systematic assessment of models of coagulation, using large dataset inputs, points to ways in which these models can be improved. A model that accurately reflects the effects of the multiple subtle variations in an individual's hemostatic profile could be used for assessing antithrombotics or as a tool for precision medicine.

Diagnosis and management of Achilles tendon ailments: the Scottish mist.

The diagnosis and management of Achilles tendon ailments continue to be widely discussed by the scientific community. Also, the nomenclature used to describe the tendinopathic lesion in patients changed over the last decades together with the evolution in the knowledge of the physiopathology of Achilles tendinopathy, and unfortunately, through ignorance and possibly laziness, confusion still abounds. To emerge from these foggy paths, some clarifications are still necessary. The present Editorial tries to clarify some of these issues.

Primary Rotator Cuff Bridging Reconstruction Shows Better Clinical and Radiographic Results Than Revision Bridging Reconstruction.

Purpose: To evaluate the outcome of revision rotator cuff bridging reconstruction (BR) as compared to primary BR in a large cohort of patients. Methods: A retrospective chart review was conducted for patients who underwent BR using dermal allograft for large/massive rotator cuff tears between 2010 and 2018. Patients who completed Western Ontario Rotator Cuff Index (WORC) and Disability of the Arm, Shoulder, and Hand (DASH) scores both pre- and postoperatively were included. Pre- and postoperative magnetic resonance imaging scans were compared to assess for differences in fatty infiltration, muscle atrophy, and graft status. Results: Eighty patients met the inclusion criteria, including 43 patients who underwent BR as a primary surgery and 37 patients who underwent revision BR. The mean follow-up duration was 5.7 ± 1.9 years in the primary group and 5.8 ± 2.0 years in the revision group. Both WORC and DASH scores significantly improved from pre- to postoperatively for both the primary and revision groups (P < .05). The primary group had significantly better postoperative WORC and DASH scores at 6 months, 1 year, and final follow-up (P < .05). Failure rate of the graft was higher in the revision group compared to primary group (14.3% vs 6.1%, respectively; P = .337), and the amount of fatty infiltration of supraspinatus and infraspinatus muscles significantly improved in patients who received primary BR compared to revision BR (P < .05). Conclusions: BR using dermal allograft for large/massive irreparable rotator cuff tears showed improvement of functional outcomes, with primary cases resulting in better improvement in patient-reported outcomes compared to revision cases. Primary BR was also associated with better postoperative fatty infiltration of supraspinatus and infraspinatus muscles. Level of Evidence: Level III, retrospective cohort study.

Sperm proteomic landscape is altered in breeding bulls with greater sperm DNA fragmentation index.

Although, it is well understood that sperm DNA damage is associated with infertility, the molecular details of how damaged sperm DNA affects fertility are not fully elucidated. Since sperm proteins play an important role in fertilization and post-fertilization events, the present study aimed to identify the sperm proteomic alterations in bulls with high sperm DNA Fragmentation Index (DFI%). Semen from Holstein-Friesian crossbred breeding bulls (n = 50) was subjected to Sperm Chromatin Structure Assay. Based on DFI%, bulls were classified into either high- (HDFI; n = 6), or low-DFI (LDFI; n = 6) and their spermatozoa were subjected to high throughput proteomic analysis. Liquid chromatography and mass spectrometry analysis identified 4567 proteins in bull spermatozoa. A total of 2660 proteins were found common to both the groups, while 1193 and 714 proteins were unique to HDFI and LDFI group, respectively. A total of 265 proteins were up regulated and 262 proteins were down regulated in HDFI group. It was found that proteins involved in capacitation [heparin binding (molecular function), ERK1 and ERK2 cascade (biological process), PI3K-Akt signalling (pathway), Jak-STAT signalling (pathway)], spermatogenesis [TLR signalling (pathway), gamete generation (biological process)] and DNA repair mechanism (biological process) were significantly altered in the bulls with high DFI%.

Fluctuations in auxin levels depend upon synchronicity of cell divisions in a one-dimensional model of auxin transport.

Auxin is a well-studied plant hormone, the spatial distribution of which remains incompletely understood. Here, we investigate the effects of cell growth and divisions on the dynamics of auxin patterning, using a combination of mathematical modelling and experimental observations. In contrast to most prior work, models are not designed or tuned with the aim to produce a specific auxin pattern. Instead, we use well-established techniques from dynamical systems theory to uncover and classify ranges of auxin patterns as exhaustively as possible as parameters are varied. Previous work using these techniques has shown how a multitude of stable auxin patterns may coexist, each attainable from a specific ensemble of initial conditions. When a key parameter spans a range of values, these steady patterns form a geometric curve with successive folds, often nicknamed a snaking diagram. As we introduce growth and cell division into a one-dimensional model of auxin distribution, we observe new behaviour which can be explained in terms of this diagram. Cell growth changes the shape of the snaking diagram, and this corresponds in turn to deformations in the patterns of auxin distribution. As divisions occur this can lead to abrupt creation or annihilation of auxin peaks. We term this phenomenon 'snake-jumping'. Under rhythmic cell divisions, we show how this can lead to stable oscillations of auxin. We also show that this requires a high level of synchronisation between cell divisions. Using 18 hour time-lapse imaging of the auxin reporter DII:Venus in roots of Arabidopsis thaliana, we show auxin fluctuates greatly, both in terms of amplitude and periodicity, consistent with the snake-jumping events observed with non-synchronised cell divisions. Periodic signals downstream of the auxin signalling pathway have previously been recorded in plant roots. The present work shows that auxin alone is unlikely to play the role of a pacemaker in this context.

Presentation and Management of the Pediatric Trigger Finger: A Multicenter Retrospective Cohort Study.

PURPOSE: Pediatric trigger finger (PTF) is an acquired condition that is uncommon and anatomically complex. Currently, the literature is characterized by a small number of retrospective case series with limited sample sizes. This investigation sought to evaluate the presentation, management, and treatment outcomes of PTF in a large, multicenter cohort. METHODS: A retrospective review of pediatric patients with a diagnosis of PTF between 2009 and 2020 was performed at three tertiary referral hospitals. Patient demographics, PTF characteristics, treatment strategies, and outcomes were abstracted from the electronic medical records. Patients and families also were contacted by telephone to assess the downstream persistence or recurrence of triggering symptoms. RESULTS: In total, 321 patients with 449 PTFs were included at a mean follow-up of 3.9 ± 4.0 years. There were approximately equal numbers of boys and girls, and the mean age of symptom onset was 5.4 ± 5.1 years. The middle (34.7%) and index (11.6%) fingers were the most and least commonly affected digits, respectively. Overall, PTFs managed operatively achieved significantly higher rates of complete resolution compared with PTFs managed nonsurgically (97.1% vs 30.0%). Seventy-five percent of PTFs that achieved complete resolution with nonsurgical management did so within 6 months, and approximately 90% did so within 12 months. Patients with multidigit involvement, higher Quinnell grade at presentation, or palpable nodularity were significantly more likely to undergo surgery. There was no significant difference in the rate of complete resolution between splinted versus not splinted PTFs or across operative techniques. CONCLUSIONS: Only 30% of the PTFs managed nonsurgically achieved complete resolution. Splinting did not improve resolution rates in children treated nonsurgically. In contrast, surgical intervention has a high likelihood of restoring motion and function of the affected digit. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic IV.

Establishment of a repertoire of fertility associated sperm proteins and their differential abundance in buffalo bulls (Bubalus bubalis) with contrasting fertility.

Sperm harbours a wide range of proteins regulating their functions and fertility. In the present study, we made an effort to characterize and quantify the proteome of buffalo bull spermatozoa, and to identify fertility associated sperm proteins through comparative proteomics. Using high-throughput mass spectrometry platform, we identified 1305 proteins from buffalo spermatozoa and found that these proteins were mostly enriched in glycolytic process, mitochondrial respiratory chain, tricarboxylic acid cycle, protein folding, spermatogenesis, sperm motility and sperm binding to zona pellucida (p < 7.74E-08) besides metabolic (p = 4.42E-31) and reactive oxygen species (p = 1.81E-30) pathways. Differential proteomic analysis revealed that 844 proteins were commonly expressed in spermatozoa from both the groups while 77 and 52 proteins were exclusively expressed in high- and low-fertile bulls, respectively. In low-fertile bulls, 75 proteins were significantly (p < 0.05) upregulated and 176 proteins were significantly (p < 0.05) downregulated; these proteins were highly enriched in mitochondrial respiratory chain complex I assembly (p = 2.63E-07) and flagellated sperm motility (p = 7.02E-05) processes besides oxidative phosphorylation pathway (p = 6.61E-15). The down regulated proteins in low-fertile bulls were involved in sperm motility, metabolism, sperm-egg recognition and fertilization. These variations in the sperm proteome could be used as potential markers for the selection of buffalo bulls for fertility.

High-throughput proteomic characterization of seminal plasma from bulls with contrasting semen quality.

Seminal plasma proteins are the major extrinsic factors that can modulate the sperm quality and functions. The present study was carried out to compare the proteomic profiles of seminal plasma from breeding bulls producing good and poor quality semen in an effort to understand the possible proteins associated with semen quality. A total of 910 and 715 proteins were detected in the seminal plasma of poor and good quality semen producing bulls, respectively. A total of 705 proteins were common to both the groups, in which 380 proteins were upregulated and 89 proteins were downregulated in the seminal plasma of poor quality semen, while 236 proteins were co-expressed. The proteins negatively influencing sperm functions such as CCL2, UQCRC2, and SAA1 were among the top ten upregulated proteins in the seminal plasma of poor quality semen. Proteins having a positive role in sperm functions (NGF, EEF1A2, COL1A2, IZUMO4, PRSS1, COL1A1, WFDC2) were among the top ten downregulated proteins in the seminal plasma of poor quality semen. The upregulation of oxidation-reduction process-related proteins, histone proteins (HIST3H2A, H2AFJ, H2AFZ, H2AFX, HIST2H2AB, H2AFV, HIST1H2AC, HIST2H2AC, LOC104975684, LOC524236, LOC614970, LOC529277), and ubiquinol-cytochrome-c reductase proteins (UQCRB, UQCRFS1, UQCRQ, UQCRC1, UQCRC2) indicate deranged oxidation-reduction equilibrium, chromatin condensation and spermatogenesis in poor quality semen producing bulls. The expression of proteins essential for motile cilium (CCDC114, CFAP206, TEKT4), chromatin integrity (PRM2), gamete fusion (IZUMO4, EQTN), hyperactivation, tyrosine phosphorylation, and capacitation [PI3K-Akt signalling pathway-related proteins (COL1A1, COL2A1, COL1A2, SPP1, PDGFA, NGF)] were down regulated in poor quality semen producing bulls. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03474-6.

Case-based discussion: neonates on extracorporeal membrane oxygenation for undiagnosed recalcitrant pulmonary hypertension-management challenges.

We present two neonates requiring extracorporeal membrane oxygenation for undiagnosed recalcitrant pulmonary hypertension, highlighting the clinical and ethical dilemmas in management of very rare diseases.

Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (Bos taurus × Bos indicus) bull spermatozoa.

Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca2++ ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including TPT1, BOLA-DRA, CD74, RPS17, RPS28, RPS29, RPL14, RPL13, and RPS27A, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.

The cryopreservation process induces alterations in proteins associated with bull sperm quality: The equilibration process could be a probable critical control point.

The present study quantitatively characterized the proteomic changes in bull spermatozoa induced by the cryopreservation process. We performed high-throughput comparative global proteomic profiling of freshly ejaculated (before cryopreservation), equilibrated (refrigerated storage; during cryopreservation), and frozen (ultralow temperature; after cryopreservation) bull spermatozoa. Using the liquid chromatography-mass spectrometry (LC-MS/MS) technique, a total of 1,692, 1,415, and 1,286 proteins were identified in fresh, equilibrated, and cryopreserved spermatozoa, respectively. When the proteome of fresh spermatozoa was compared with equilibrated spermatozoa, we found that 166 proteins were differentially expressed. When equilibrated spermatozoa were compared with cryopreserved spermatozoa, we found that 147 proteins were differentially expressed between them. Similarly, we found that 156 proteins were differentially expressed between fresh and cryopreserved spermatozoa. Among these proteins, the abundance of 105 proteins was lowered during the equilibration process itself, while the abundance of 43 proteins was lowered during ultralow temperature preservation. Remarkably, the equilibration process lowered the abundance of sperm proteins involved in energy metabolism, structural integrity, and DNA repair and increased the abundance of proteins associated with proteolysis and protein degradation. The abundance of sperm proteins associated with metabolism, cGMP-PKG (cyclic guanosine 3',5'-monophosphate-dependent protein kinase G) signaling, and regulation of the actin cytoskeleton was also altered during the equilibration process. Collectively, the present study showed that the equilibration step in the bull sperm cryopreservation process was the critical point for sperm proteome, during which a majority of proteomic alterations in sperm occurred. These findings are valuable for developing efficient protocols to minimize protein damage and to improve the quality and fertility of cryopreserved bull spermatozoa.

The impact of a metal artefact reduction algorithm on treatment planning for patients undergoing radiotherapy of the pelvis.

Background and purpose: Metallic implants cause artefacts in computed tomography (CT) images and can introduce significant errors to structure visualisation and dosimetric calculation within the radiotherapy planning process. This study evaluated an orthopaedic metal artefact reduction algorithm and its effect on the CT number, image noise, structure delineation, and treatment dose. Methods: Raw CT data were reconstructed using standard filtered back projection and an artefact reduction algorithm to create 'standard' and 'corrected' images. A phantom containing tissue-mimicking inserts and two titanium plugs was imaged. The average CT number was compared to baseline data acquired without metal inserts. Data from 11 pelvic external beam radiotherapy (EBRT) patients with bi- or uni-lateral hip implants were retrospectively analysed. The clinically used treatment plans were re-computed on the corrected images. A prostate-mimicking phantom containing metal 'implants' was imaged, and 11 observers contoured both reconstructions. Results: The artefact reduction algorithm improved the CT number in those areas most affected by metal artefacts and decreased noise by 19 % (P =.04) Changes in dose distributions on corrected images compared to those calculated using the current clinical protocol were clinically insignificant. Volumes contoured on the corrected phantom images had larger Dice coefficients than those contoured on the standard images (P =.001), as well as a 36 % lower standard deviation in volumes. Conclusion: This study demonstrates that the metal artefact reduction software reduces the error in CT numbers, can improve delineation accuracy, and can reduce inter-observer variability. It has the potential to streamline the planning pathway and improve treatment planning accuracy.

Cryopreservation process alters the expression of genes involved in pathways associated with the fertility of bull spermatozoa.

In bovines, cryopreserved semen is used for artificial insemination; however, the fertility of cryopreserved semen is far lower than that of fresh semen. Although cryopreservation alters sperm phenotypic characteristics, its effect on sperm molecular health is not thoroughly understood. The present study applied next-generation sequencing to investigate the effect of cryopreservation on the sperm transcriptomic composition of bull spermatozoa. While freshly ejaculated bull spermatozoa showed 14,280 transcripts, cryopreserved spermatozoa showed only 12,375 transcripts. Comparative analysis revealed that 241 genes were upregulated, 662 genes were downregulated, and 215 genes showed neutral expression in cryopreserved spermatozoa compared to fresh spermatozoa. Gene ontology analysis indicated that the dysregulated transcripts were involved in nucleic acid binding, transcription-specific activity, and protein kinase binding involving protein autophosphorylation, ventricular septum morphogenesis, and organ development. Moreover, the dysregulated genes in cryopreserved spermatozoa were involved in pathways associated with glycogen metabolism, MAPK signalling, embryonic organ morphogenesis, ectodermal placode formation, and regulation of protein auto-phosphorylation. These findings suggest that the cryopreservation process induced alterations in the abundance of sperm transcripts related to potential fertility-associated functions and pathways, which might partly explain the reduced fertility observed with cryopreserved bull spermatozoa.

Pseudomonas aeruginosa in the Cystic Fibrosis Lung.

Cystic fibrosis is a common genetically inherited, multisystem disorder caused by loss of function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, an apically situated anion channel. In the lung, lack of CFTR leads to airway surface dehydration, mucociliary clearance failure and an acidic pH in which innate defence molecules are rendered ineffective. Infection occurs early in life, with P. aeruginosa dominating by adolescence. The characteristic features of the CF airway highlighted above encourage persistence of infection, but P. aeruginosa also possess an array of mechanisms with which they attack host defences and render themselves protected from antimicrobials. Early eradication is usually successful, but this is usually transient. Chronic infection is manifest by biofilm formation which is resistant to treatment. Outcomes for people with CF have improved greatly in the last few decades, but particularly so with the recent advent of small molecule CFTR modulators. However, despite impressive efficacy on lung function and exacerbation frequency, most people with chronic infection remain with their pathogens. There is an active pipeline of new treatments including anti-biofilm and anti-quorum sensing molecules and non-drug approaches such as bacteriophage. Studies are reviewed and challenges for future drug development considered.

Public Interest Group on Cancer Research: a successful patient-researcher partnership in Newfoundland and Labrador.

BACKGROUND: Partnering with patients and family members affected by cancer is essential for meaningful research, public engagement and outreach, and advocacy activities. OBJECTIVE: Our objective was to create a public interest group through an academic-community partnership focused on cancer research and public engagement. METHODS: A purposeful recruitment process was implemented to ensure a diverse and inclusive group. The group meets virtually and communicates by email. The group's activities focus on identifying the needs, priorities, and interests of cancer-affected individuals in the province; consultations; and designing research projects and public outreach activities together. Comprehensive meeting minutes are kept and used to distill discussion points. The work of the group is disseminated through a variety of channels. RESULTS: The public interest group includes 12 cancer patient and family member representatives, in addition to researchers. Discussions by the interest group identified key themes related to: (1) equity issues and regional disparity in provincial oncocare; (2) information needs; (3) need for patient empowerment and public understanding; and (4) family member and partner needs and experiences. To date, the group has co-designed a cancer research proposal and a public engagement/outreach activity. The group also provides consultations on cancer-related projects/public engagement activities and members act as patient partners in specific research and public engagement proposals. The group evolves over time, and increasingly advocates on behalf of cancer patients and families. Retention and satisfaction of the public partners with group activities have been high. The group's work and findings are disseminated to the Provincial Cancer Care Program, as well as to public and scientific stakeholders through local media, academic conferences and presentations, and a dedicated website. CONCLUSION: Public Interest Group on Cancer Research represents a highly successful patient-researcher partnership in oncology. It designs meaningful and patient-oriented studies and outreach activities in cancer. It also elevates and widely supports cancer patient and family voice.

Cancer patients and their family members have unique and lived experience with the condition. Therefore, collaborating with them is important in cancer science. We aimed to create such a collaboration in Newfoundland and Labrador, Canada. In 2021, we successfully formed our diverse collaborative group. Currently, our group includes 12 public representatives. We meet online and discuss matters important to members. We also design studies and events together. Our discussions have identified four topics that need further research and policy changes such as information needs and unique needs of caregivers and family members. Our activities expand over time. For example, lately we started to advocate for other cancer patients and families. In conclusion, we formed a successful cancer patient, family member, and researcher collaborative group. Our work informs the public, healthcare systems, and scientists on important cancer related matters.

Cavity-Amplified Scattering Spectroscopy Reveals the Dynamics of Proteins and Nanoparticles in Quasi-transparent and Miniature Samples.

Dynamic light scattering techniques can give access to the motion spectrum of microscopic objects and are therefore routinely used for numerous industrial and research applications ranging from particle sizing to the characterization of the viscoelastic properties of materials. However, such measurements are impossible when samples do not scatter light enough, i.e., when light undergoes too few scattering events when passing through a sample, either due to excessively small scattering cross sections or due to low concentrations of scatterers. Here, we propose to amplify the light scattering efficiency by placing weakly scattering samples inside a Lambertian cavity with high-reflectance walls. When injected with laser light, the cavity produces a 3D isotropic and homogeneous light field, effectively elongates the photon scattering path length through the sample by 2-3 orders of magnitude, and leads to a dramatic increase in sensitivity. With a 104-fold increase in sensitivity compared to classical techniques, we potentially expand the applications of light scattering to miniaturized microfluidics samples and to weakly scattering samples in general. We show that we can access the short-time dynamics of low-turbidity samples and demonstrate our sensitivity gain by measuring the diffusion coefficient and, therefore, the size of particles ranging from 5 nm to 20 µm with volume fractions as low as 10-9 in volumes as low as 100 µL and in solvents with refractive index mismatches down to Δn ≈ 0.01. Beyond the realm of current applications of light scattering techniques, our cavity-amplified scattering spectroscopy method (CASS) and its high sensitivity represent a significant methodological step toward the study of short-time dynamics problems such as the ballistic limit of Brownian motion, the internal dynamics of proteins, or the dielectric dynamics of liquids.

Assessing mild cognitive impairment using object-location memory in immersive virtual environments.

Pathological changes in the medial temporal lobe (MTL) are found in the early stages of Alzheimer's disease (AD) and aging. The earliest pathological accumulation of tau colocalizes with the areas of the MTL involved in object processing as part of a wider anterolateral network. Here, we sought to assess the diagnostic potential of memory for object locations in iVR environments in individuals at high risk of AD dementia (amnestic mild cognitive impairment [aMCI] n = 23) as compared to age-related cognitive decline. Consistent with our primary hypothesis that early AD would be associated with impaired object location, aMCI patients exhibited impaired spatial feature binding. Compared to both older (n = 24) and younger (n = 53) controls, aMCI patients, recalled object locations with significantly less accuracy (p < .001), with a trend toward an impaired identification of the object's correct context (p = .05). Importantly, these findings were not explained by deficits in object recognition (p = .6). These deficits differentiated aMCI from controls with greater accuracy (AUC = 0.89) than the standard neuropsychological tests. Within the aMCI group, 16 had CSF biomarkers indicative of their likely AD status (MCI+ n = 9 vs. MCI- n = 7). MCI+ showed lower accuracy in the object-context association than MCI- (p = .03) suggesting a selective deficit in object-context binding postulated to be associated with anterior-temporal areas. MRI volumetric analysis across healthy older participants and aMCI revealed that test performance positively correlates with lateral entorhinal cortex volumes (p < .05) and hippocampus volumes (p < .01), consistent with their hypothesized role in binding contextual and spatial information with object identity. Our results indicate that tests relying on the anterolateral object processing stream, and in particular requiring successful binding of an object with spatial information, may aid detection of pre-dementia AD due to the underlying early spread of tau pathology.

Metabolic modeling-based drug repurposing in Glioblastoma.

The manifestation of intra- and inter-tumor heterogeneity hinders the development of ubiquitous cancer treatments, thus requiring a tailored therapy for each cancer type. Specifically, the reprogramming of cellular metabolism has been identified as a source of potential drug targets. Drug discovery is a long and resource-demanding process aiming at identifying and testing compounds early in the drug development pipeline. While drug repurposing efforts (i.e., inspecting readily available approved drugs) can be supported by a mechanistic rationale, strategies to further reduce and prioritize the list of potential candidates are still needed to facilitate feasible studies. Although a variety of 'omics' data are widely gathered, a standard integration method with modeling approaches is lacking. For instance, flux balance analysis is a metabolic modeling technique that mainly relies on the stoichiometry of the metabolic network. However, exploring the network's topology typically neglects biologically relevant information. Here we introduce Transcriptomics-Informed Stoichiometric Modelling And Network analysis (TISMAN) in a recombinant innovation manner, allowing identification and validation of genes as targets for drug repurposing using glioblastoma as an exemplar.

Central tropical Pacific convection drives extreme high temperatures and surface melt on the Larsen C Ice Shelf, Antarctic Peninsula.

Northern sections of the Larsen Ice Shelf, eastern Antarctic Peninsula (AP) have experienced dramatic break-up and collapse since the early 1990s due to strong summertime surface melt, linked to strengthened circumpolar westerly winds. Here we show that extreme summertime surface melt and record-high temperature events over the eastern AP and Larsen C Ice Shelf are triggered by deep convection in the central tropical Pacific (CPAC), which produces an elongated cyclonic anomaly across the South Pacific coupled with a strong high pressure anomaly over Drake Passage. Together these atmospheric circulation anomalies transport very warm and moist air to the southwest AP, often in the form of "atmospheric rivers", producing strong foehn warming and surface melt on the eastern AP and Larsen C Ice Shelf. Therefore, variability in CPAC convection, in addition to the circumpolar westerlies, is a key driver of AP surface mass balance and the occurrence of extreme high temperatures.

Integrated multi-omics analyses reveals molecules governing sperm metabolism potentially influence bull fertility.

Bull fertility is of paramount importance in bovine industry because semen from a single bull is used to breed several thousands of cows; however, so far, no reliable test is available for bull fertility prediction. In the present study, spermatozoa from high- and low-fertility bulls were subjected to high-throughput transcriptomic, proteomic and metabolomic analysis. Using an integrated multi-omics approach the molecular differences between high- and low-fertility bulls were identified. We identified a total of 18,068 transcripts, 5041 proteins and 3704 metabolites in bull spermatozoa, of which the expression of 4766 transcripts, 785 proteins and 33 metabolites were dysregulated between high- and low-fertility bulls. At transcript level, several genes involved in oxidative phosphorylation pathway were found to be downregulated, while at protein level genes involved in metabolic pathways were significantly downregulated in low-fertility bulls. We found that metabolites involved in Taurine and hypotaurine metabolism were significantly downregulated in low-fertility bulls. Integrated multi-omics analysis revealed the interaction of dysregulated transcripts, proteins and metabolites in major metabolic pathways, including Butanoate metabolism, Glycolysis and gluconeogenesis, Methionine and cysteine metabolism, Phosphatidyl inositol phosphate, pyrimidine metabolism and saturated fatty acid beta oxidation. These findings collectively indicate that molecules governing sperm metabolism potentially influence bull fertility.