Metal-Metal Bonding in Actinide Dimers: U2 and U2.

Understanding direct metal-metal bonding between actinide atoms has been an elusive goal in chemistry for years. We report for the first time the anion photoelectron spectrum of U2-. The threshold of the lowest electron binding energy (EBE) spectral band occurs at 1.0 eV, which corresponds to the electron affinity (EA) of U2, whereas the vertical detachment energy of U2- is found at EBE ∼ 1.2 eV. Electronic structure calculations on U2 and U2- were carried out with state-of-the-art theoretical methods. The computed values of EA(U2) and EA(U) and the difference between the computed dissociation energies of U2 and U2- are found to be internally consistent and consistent with experiment. Analysis of the bonds in U2 and U2- shows that while U2 has a formal quintuple bond, U2- has a quadruple bond, even if the effective bond orders differ only by 0.5 unit instead of one unit. The resulting experimental-computational synergy elucidates the nature of metal-metal bonding in U2 and U2-.

Core Set of Patient-reported Outcomes in Pancreatic Cancer (COPRAC): An International Delphi Study Among Patients and Health Care Providers.

OBJECTIVE: To establish an international core set of patient-reported outcomes (PROs) selected by both patients and healthcare providers (HCPs) from the United States (US), Europe, and Asia. SUMMARY BACKGROUND DATA: PROs are increasingly recognized in pancreatic cancer studies. There is no consensus on which of the many available PROs are most important. METHODS: A multicenter Delphi study among patients with pancreatic cancer (curative- and palliative-setting) and HCPs in 6 pancreatic centers in the US (Baltimore, Boston), Europe (Amsterdam, Verona), and Asia (Mumbai, Seoul) was performed. In round 1, participants rated the importance of 56 PROs on a 1 to 9 Likert scale. PROs rated as very important (scores 7-9) by the majority (≥80%) of curative- and/or palliative-patients as well as HCPs were included in the core set. PROs not fulfilling these criteria were presented again in round 2, together with feedback on individual and group ratings. Remaining PROs were ranked based on the importance ratings. RESULTS: In total 731 patients and HCPs were invited, 501 completed round 1, and 420 completed both rounds. This included 204 patients in curative-setting, 74 patients in palliative-setting, and 142 HCPs. After 2 rounds, 8 PROs were included in the core set: general quality of life, general health, physical ability, ability to work/do usual activities, fear of recurrence, satisfaction with services/care organization, abdominal complaints, and relationship with partner/family. CONCLUSIONS: This international Delphi study among patients and HCPs established a core set of PROs in pancreatic cancer, which should facilitate the design of future pancreatic cancer trials and outcomes research.

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.

Hematopoietic stem and progenitor cells (HSPCs) are vulnerable to endogenous damage and defects in DNA repair can limit their function. The 2 single-stranded DNA (ssDNA) binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response; however, their overlapping roles during normal physiology are incompletely understood. We generated mice in which both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, whereas conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featuring stem and progenitor cell depletion, a phenotype unexpected from the previously reported single knockout models of Ssb1 or Ssb2 Mechanistically, cDKO HSPCs showed altered replication fork dynamics, massive accumulation of DNA damage, genome-wide double-strand breaks enriched at Ssb-binding regions and CpG islands, together with the accumulation of R-loops and cytosolic ssDNA. Transcriptional profiling of cDKO HSPCs revealed the activation of p53 and interferon (IFN) pathways, which enforced cell cycling in quiescent HSPCs, resulting in their apoptotic death. The rapid cell death phenotype was reproducible in in vitro cultured cDKO-hematopoietic stem cells, which were significantly rescued by nucleotide supplementation or after depletion of p53. Collectively, Ssb1 and Ssb2 control crucial aspects of HSPC function, including proliferation and survival in vivo by resolving replicative stress to maintain genomic stability.

Extended pancreatectomy as defined by the ISGPS: useful in selected cases of pancreatic cancer but invaluable in other complex pancreatic tumors.

PURPOSE: Extended pancreatectomy aimed at R0 resection of pancreatic tumors with adjacent vessel and organ involvement may be the only option for cure. This study was done with an objective to analyze the short- and long-term outcomes of extended pancreatic resections. METHODS: All pancreatectomies performed between 2006 and 2015 were included. The pancreatectomies were classified as standard or extended, as per the International Study Group for Pancreatic Surgery. All surgical complications and terminologies were according to Clavien-Dindo classification and International Study Group for Pancreatic Surgery guidelines. Morbidity and mortality were primary outcomes and disease-free survival was a secondary outcome. RESULTS: Sixty-three extended and 620 standard pancreatectomies were performed. Major morbidity (Clavien grades III, IV and V) (37 vs. 29%, p = 0.21) and mortality (6 vs. 4%, p = 0.3) for extended pancreatectomies were comparable to those for standard pancreatectomies. Blood loss > 855 ml, need for blood transfusion, and tumor size were independent risk factors for morbidity, and the latter two for mortality. Standard pancreatectomies were associated with better 3-year disease-free survival than extended pancreatectomies (67 vs. 41%, p < 0.001). Extended pancreatectomies resulted in a significantly better median disease-free survival for non-pancreatic adenocarcinoma vs. pancreatic adenocarcinoma (33.3 vs. 9.5 months, p = 0.01). CONCLUSION: Extended pancreatectomies resulted in similar peri-operative morbidity and mortality compared to standard pancreatectomies. Although the survival of patients undergoing these complex procedures is inferior to standard pancreatectomies, they should be undertaken not only in selected cases of pancreatic cancer but even more so in other complex pancreatic tumors.

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.

We present a genome-wide approach to map DNA double-strand breaks (DSBs) at nucleotide resolution by a method we termed BLESS (direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing). We validated and tested BLESS using human and mouse cells and different DSBs-inducing agents and sequencing platforms. BLESS was able to detect telomere ends, Sce endonuclease-induced DSBs and complex genome-wide DSB landscapes. As a proof of principle, we characterized the genomic landscape of sensitivity to replication stress in human cells, and we identified >2,000 nonuniformly distributed aphidicolin-sensitive regions (ASRs) overrepresented in genes and enriched in satellite repeats. ASRs were also enriched in regions rearranged in human cancers, with many cancer-associated genes exhibiting high sensitivity to replication stress. Our method is suitable for genome-wide mapping of DSBs in various cells and experimental conditions, with a specificity and resolution unachievable by current techniques.

Modulation of gene expression regulated by the transcription factor NF-κB/RelA.

Modulators (Ms) are proteins that modify the activity of transcription factors (TFs) and influence expression of their target genes (TGs). To discover modulators of NF-κB/RelA, we first identified 365 NF-κB/RelA-binding proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We used a probabilistic model to infer 8349 (M, NF-κB/RelA, TG) triplets and their modes of modulatory action from our combined LC-MS/MS and ChIP-Seq (ChIP followed by next generation sequencing) data, published RelA modulators and TGs, and a compendium of gene expression profiles. Hierarchical clustering of the derived modulatory network revealed functional subnetworks and suggested new pathways modulating RelA transcriptional activity. The modulators with the highest number of TGs and most non-random distribution of action modes (measured by Shannon entropy) are consistent with published reports. Our results provide a repertoire of testable hypotheses for experimental validation. One of the NF-κB/RelA modulators we identified is STAT1. The inferred (STAT1, NF-κB/RelA, TG) triplets were validated by LC-selected reaction monitoring-MS and the results of STAT1 deletion in human fibrosarcoma cells. Overall, we have identified 562 NF-κB/RelA modulators, which are potential drug targets, and clarified mechanisms of achieving NF-κB/RelA multiple functions through modulators. Our approach can be readily applied to other TFs.

Neoadjuvant chemotherapy in patients with locally advanced gallbladder cancer.

AIM: Surgery is the only curative option for patients with gallbladder cancer (GBC). This study looks at the outcome of patients treated with neoadjuvant chemotherapy (NACT). PATIENTS & METHODS: This is retrospective analysis of the prospectively maintained database of patients with locally advanced GBC treated between February 2009 and September 2013 with NACT. Patients received gemcitabine-platinum based regimen. RESULTS: A total of 37 patients (median age: 54 years, 64.9% females) received NACT. Overall response rate was 67.5%. In total, 17 patients (46%) underwent R0 resection. Median overall survival/progression-free survival of the whole group was 13.4/8.1 months, respectively. Patients who underwent surgery had a significantly better overall survival (median not reached vs 9.5 months) and progression-free survival (25.8 vs 5.6 months), respectively. CONCLUSION: NACT increases resectability and survival in patients with locally advanced GBC.

A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-Seq.

Using nuclear factor-κB (NF-κB) ChIP-Seq data, we present a framework for iterative learning of regulatory networks. For every possible transcription factor-binding site (TFBS)-putatively regulated gene pair, the relative distance and orientation are calculated to learn which TFBSs are most likely to regulate a given gene. Weighted TFBS contributions to putative gene regulation are integrated to derive an NF-κB gene network. A de novo motif enrichment analysis uncovers secondary TFBSs (AP1, SP1) at characteristic distances from NF-κB/RelA TFBSs. Comparison with experimental ENCODE ChIP-Seq data indicates that experimental TFBSs highly correlate with predicted sites. We observe that RelA-SP1-enriched promoters have distinct expression profiles from that of RelA-AP1 and are enriched in introns, CpG islands and DNase accessible sites. Sixteen novel NF-κB/RelA-regulated genes and TFBSs were experimentally validated, including TANK, a negative feedback gene whose expression is NF-κB/RelA dependent and requires a functional interaction with the AP1 TFBSs. Our probabilistic method yields more accurate NF-κB/RelA-regulated networks than a traditional, distance-based approach, confirmed by both analysis of gene expression and increased informativity of Genome Ontology annotations. Our analysis provides new insights into how co-occurring TFBSs and local chromatin context orchestrate activation of NF-κB/RelA sub-pathways differing in biological function and temporal expression patterns.

Gastric salvage after venous congestion during major pancreatic resections: A series of three cases.

Pancreatic resections, depending on the location of the tumor, usually require division of the vasculature of either the distal or proximal part of the stomach. In certain situations, such as total pancreatectomy and/or with splenic vein occlusion, viability of the stomach may be threatened due to inadequate venous drainage. We discuss three cases of complex pancreatic surgeries performed for carcinoma of the pancreas at a tertiary care center in India, wherein the stomach was salvaged by reimplanting the veins in two patients and preserving the only draining collateral in one case after the gastric venous drainage was compromised. The perioperative and postoperative course in these patients and the complications were analyzed. None of these 3 patients developed any complication related to gastric venous congestion, and additional gastrectomy was avoided in all these patients. Re-establishment of the Gastric venous outflow after extensive pancreatic resections helps to avoid additional gastric resection secondary to venous congestive changes.

Density Matrix Embedding Using Multiconfiguration Pair-Density Functional Theory.

We present a quantum embedding method for ground and excited states of extended systems that uses multiconfiguration pair-density functional theory (MC-PDFT) with densities provided by periodic density matrix embedding theory (pDMET). We compute local excitations in oxygen mono- and divacancies on a magnesium oxide (100) surface and find absolute deviations within 0.05 eV between pDMET using the MC-PDFT, denoted as pDME-PDFT, and the more expensive, nonembedded MC-PDFT approach. We further use pDME-PDFT to calculate local excitations in larger supercells for the monovacancy defect, for which the use of nonembedded MC-PDFT is prohibitively costly.

Local Excitations of a Charged Nitrogen Vacancy in Diamond with Multireference Density Matrix Embedding Theory.

We investigate the negatively charged nitrogen-vacancy center in diamond using periodic density matrix embedding theory (pDMET). To describe the strongly correlated excited states of this system, the complete active space self-consistent field (CASSCF) followed by n-electron valence state second-order perturbation theory (NEVPT2) was used as the impurity solver. Since the NEVPT2-DMET energies show a linear dependence on the inverse of the size of the embedding subspace, we performed an extrapolation of the excitation energies to the nonembedding limit using a linear regression. The extrapolated NEVPT2-DMET first triplet-triplet excitation energy is 2.31 eV and that for the optically inactive singlet-singlet transition is 1.02 eV, both in agreement with the experimentally observed vertical excitation energies of ∼2.18 eV and ∼1.26 eV, respectively. This is the first application of pDMET to a charged periodic system and the first investigation of the NV- defect using NEVPT2 for periodic supercell models.

Optical Properties of Neutral F Centers in Bulk MgO with Density Matrix Embedding.

The optical spectra of neutral oxygen vacancies (F0 centers) in the bulk MgO lattice are investigated using density matrix embedding theory. The impurity Hamiltonian is solved with the complete active space self-consistent field and second-order n-electron valence state perturbation theory (NEVPT2-DMET) multireference methods. To estimate defect-localized vertical excitation energies at the nonembedding and thermodynamic limits, a double extrapolation scheme is employed. The extrapolated NEVPT2-DMET vertical excitation energy value of 5.24 eV agrees well with the experimental absorption maxima at 5.03 eV, whereas the excitation energy value of 2.89 eV at the relaxed triplet defect-localized state geometry overestimates the experimental emission at 2.4 eV by only nearly 0.5 eV, indicating the involvement of the triplet-singlet decay pathway.

Periodic Density Matrix Embedding for CO Adsorption on the MgO(001) Surface.

The adsorption of simple gas molecules to metal oxide surfaces is a primary step in many heterogeneous catalysis applications. Quantum chemical modeling of these reactions is a challenge in terms of both cost and accuracy, and quantum-embedding methods are promising, especially for localized chemical phenomena. In this work, we employ density matrix embedding theory (DMET) for periodic systems to calculate the adsorption energy of CO to the MgO(001) surface. Using coupled-cluster theory with single and double excitations and second-order Møller-Plesset perturbation theory as quantum chemical solvers, we perform calculations with embedding clusters up to 266 electrons in 306 orbitals, with the largest embedding models agreeing to within 1.2 kcal/mol of the non-embedding references. Moreover, we present a memory-efficient procedure of storing and manipulating electron repulsion integrals in the embedding space within the framework of periodic DMET.

Neoadjuvant therapy in borderline resectable pancreatic cancer: Outcomes in the era of changing practices and evolving evidence.

BACKGROUND: Neoadjuvant therapy (NAT) is increasingly being used in the management of borderline resectable pancreatic cancer (BRPC). We compared the outcomes of patients with BRPC treated either with upfront surgery (UPS) or NAT to assess whether increased use of NAT has helped improve perioperative and long-term outcomes. METHODS: Prospectively maintained database of 201 consecutive patients with BRPC treated at Tata Memorial Center, India, from 2007-2019 was analyzed. RESULTS: NAT was offered to 148 patients and 53 were planned for UPS. Progression on NAT was seen in 47 (31.8%) patients. Resection was performed in 103 patients (51.24%). The resection rate was significantly lower after NAT as compared with upfront explorations (42.56% vs 75.47%, P = .00) however, R0 resection rate after NAT was significantly better (74.6% vs 42.5%, P = .001). NAT group showed a significant decrease in the pT stage (P = .004), node positivity (60%-31.7%, P = .005%), and perineural invasion (70%-41.6% P = .026). There was no significant difference in the median overall survival (OS) of patients offered NAT versus UPS on an intention-to-treat basis (15 vs 18 months P = .431). However, OS (22 vs 19 months, P = .205) and disease-free survival (DFS) (16 vs 11 months, P = .135) were higher for resected patients in the NAT group and OS was significantly superior in patients completing the course of treatment (34 vs 22 months, P = .010) CONCLUSION: The progression rate with NAT in patients with BPRC was 31.8%. NAT was associated with significant pathologic downstaging, improvement in R0 resection rate, and survival in resected patients.

Excited States of Crystalline Point Defects with Multireference Density Matrix Embedding Theory.

Accurate and affordable methods to characterize the electronic structure of solids are important for targeted materials design. Embedding-based methods provide an appealing balance in the trade-off between cost and accuracy─particularly when studying localized phenomena. Here, we use the density matrix embedding theory (DMET) algorithm to study the electronic excitations in solid-state defects with a restricted open-shell Hartree-Fock (ROHF) bath and multireference impurity solvers, specifically, complete active space self-consistent field (CASSCF) and n-electron valence state second-order perturbation theory (NEVPT2). We apply the method to investigate the electronic excitations in an oxygen vacancy (OV) on a MgO(100) surface and find absolute deviations within 0.05 eV between DMET using the CASSCF/NEVPT2 solver, denoted as CAS-DMET/NEVPT2-DMET, and the nonembedded CASSCF/NEVPT2 approach. Next, we establish the practicality of DMET by extending it to larger supercells for the OV defect and a neutral silicon vacancy in diamond where the use of nonembedded CASSCF/NEVPT2 is extremely expensive.

EZH2-induced lysine K362 methylation enhances TMPRSS2-ERG oncogenic activity in prostate cancer.

The TMPRSS2-ERG gene fusion is the most frequent alteration observed in human prostate cancer. However, its role in disease progression is still unclear. In this study, we uncover an important mechanism promoting ERG oncogenic activity. We show that ERG is methylated by Enhancer of zest homolog 2 (EZH2) at a specific lysine residue (K362) located within the internal auto-inhibitory domain. Mechanistically, K362 methylation modifies intra-domain interactions, favors DNA binding and enhances ERG transcriptional activity. In a genetically engineered mouse model of ERG fusion-positive prostate cancer (Pb-Cre4 Pten flox/flox Rosa26-ERG, ERG/PTEN), ERG K362 methylation is associated with PTEN loss and progression to invasive adenocarcinomas. In both ERG positive VCaP cells and ERG/PTEN mice, PTEN loss results in AKT activation and EZH2 phosphorylation at serine 21 that favors ERG methylation. We find that ERG and EZH2 interact and co-occupy several sites in the genome forming trans-activating complexes. Consistently, ERG/EZH2 co-regulated target genes are deregulated preferentially in tumors with concomitant ERG gain and PTEN loss and in castration-resistant prostate cancers. Collectively, these findings identify ERG methylation as a post-translational modification sustaining disease progression in ERG-positive prostate cancers.

Impact of Length of Distal Margin on Outcomes Following Sphincter Preserving Surgery for Middle and Lower Third Rectal Cancers.

Outcomes of sphincter preserving surgery for distal rectal cancers improve with clear circumferential resection and distal resection margin. However, the extent of distal resection margin after a complete mesorectal excision is often a cause for debate. We evaluated the outcome of middle and lower third rectal cancer patients undergoing sphincter preservation with variable distal resection margin at our center. Patients with biopsy-proven rectal adenocarcinoma within 10 cm from anal verge undergoing sphincter preserving resections were included. Patients with positive circumferential resection margin were excluded. Patients were divided into three groups based on the extent of distal resection margin (< 6 mm, 6-10 mm, > 10 mm) and oncological outcomes were compared. The median age of 242 patients was 50 years and 44 (18.2%) were high-grade tumors. Preoperative chemoradiation was used in 185 (75.2%) patients. Median distal resection margin was 20 mm. Patients in < 10 mm group had a significantly higher proportion of lower third (68.3% vs 39.8%, p = 0.004) and chemoradiation-treated tumors (85.4 vs 74.6%, p = 0.001). A significantly higher percentage required an intersphincteric resection in the < 10 mm group (53.7% vs 14.4%, p = 0.0001). Significantly higher percentage tumors were pT3 in > 10 mm group (45.3% vs. 31.7%) (p = 0.05). The median follow-up was 23 months. There was no difference in the overall, loco-regional, and distant recurrence rates between the three groups. A subcentimeter distal resection margin does not influence loco-regional or distant recurrence rates following sphincter preserving surgery for middle and lower third rectal adenocarcinoma.

Epigenetic Control of Mitochondrial Fission Enables Self-Renewal of Stem-like Tumor Cells in Human Prostate Cancer.

Cancer stem cells (CSCs) contribute to disease progression and treatment failure in human cancers. The balance among self-renewal, differentiation, and senescence determines the expansion or progressive exhaustion of CSCs. Targeting these processes might lead to novel anticancer therapies. Here, we uncover a novel link between BRD4, mitochondrial dynamics, and self-renewal of prostate CSCs. Targeting BRD4 by genetic knockdown or chemical inhibitors blocked mitochondrial fission and caused CSC exhaustion and loss of tumorigenic capability. Depletion of CSCs occurred in multiple prostate cancer models, indicating a common vulnerability and dependency on mitochondrial dynamics. These effects depended on rewiring of the BRD4-driven transcription and repression of mitochondrial fission factor (Mff). Knockdown of Mff reproduced the effects of BRD4 inhibition, whereas ectopic Mff expression rescued prostate CSCs from exhaustion. This novel concept of targeting mitochondrial plasticity in CSCs through BRD4 inhibition provides a new paradigm for developing more effective treatment strategies for prostate cancer.

i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks.

Maintenance of genome stability is a key issue for cell fate that could be compromised by chromosome deletions and translocations caused by DNA double-strand breaks (DSBs). Thus development of precise and sensitive tools for DSBs labeling is of great importance for understanding mechanisms of DSB formation, their sensing and repair. Until now there has been no high resolution and specific DSB detection technique that would be applicable to any cells regardless of their size. Here, we present i-BLESS, a universal method for direct genome-wide DNA double-strand break labeling in cells immobilized in agarose beads. i-BLESS has three key advantages: it is the only unbiased method applicable to yeast, achieves a sensitivity of one break at a given position in 100,000 cells, and eliminates background noise while still allowing for fixation of samples. The method allows detection of ultra-rare breaks such as those forming spontaneously at G-quadruplexes.

Improved Outcomes in 394 Pancreatic Cancer Resections: the Impact of Enhanced Recovery Pathway.

BACKGROUND: Enhanced recovery (ER) pathway reduces morbidity and accelerates recovery. It is associated with reduced postoperative stay, morbidity, and costs. Feasibility and safety of ER programme has not been studied in developing countries. The objectives were to assess compliance with Enhanced Recovery After Surgery (ERAS) elements and to assess outcomes in pancreatic surgery. METHODS: Prospective study conducted from February 2014 to December 2016, following elective pancreatic cancer surgery. Team was educated prior to implementation of ERAS. Patients were followed up until 30 days postoperatively or discharge. Data was recorded regarding the compliance with the protocol, functional GI recovery, mobilisation, and postoperative morbidity and mortality. RESULTS: A total of 394 patients underwent surgery. Compliance with ER elements implemented was 84% (23-100%). Compliance > 80% with ER elements was observed in 278 patients (70.5%) and < 80% in 116 patients (29.5%). Patients with > 80% compliance have significantly lower major complications (28.7 vs. 44%, p = 0.001), mortality (2.1 vs. 6.8%, p = 0.021), and postoperative stay (11 (5-78) days vs. 15 (4-61) days, p < 0.001). CONCLUSION: ER programme is feasible and safe in resource and infrastructure limited lower middle-income country. Improved compliance was associated with reduced major complications, mortality, and shorter stay in patients undergoing pancreatic cancer surgery in high-volume centre. TRIAL REGISTRATION: CTRI/2015/01/005393 ( www.ctri.nic.in ).