Extracting Scattering Phase-Shifts in Higher Partial-Waves from Lattice QCD Calculations

L\"uscher's method is routinely used to determine meson-meson, meson-baryon and baryon-baryon s-wave scattering amplitudes below inelastic thresholds from Lattice QCD calculations - presently at unphysical light-quark masses. In this work we review the formalism and develop the requisite expressions to extract phase-shifts describing meson-meson scattering in partial-waves with angular-momentum l<=6 and l=9. The implications of the underlying cubic symmetry, and strategies for extracting the phase-shifts from Lattice QCD calculations, are presented, along with a discussion of the signal-to-noise problem that afflicts the higher partial-waves.Comment: 79 pages, 41 figure

A review on life cycle environmental impacts of emerging solar cells

The development of solar technologies requires increased efficiency in converting solar radiation to energy, as well as innovative materials and structure to go beyond the conventional power conversion ratio. In line with these innovations, there are concerns about greenhouse gas emissions of the solar cells, materials for the solar technologies and other relevant environmental impacts of the manufacturing processes. This review is conducted on life cycle assessments of solar cells, considering the climate change and natural resource shortage context. It is identified that the majority of existing life cycle assessments on solar cells take into account four typical environmental impacts: energy consumption, greenhouse gas emissions, material depletion, and toxicity. Though the diverse methodological aspects make it difficult to directly compare these environmental impacts among various types of solar cells, the obtained results hinder that emerging solar cells such as perovskite solar cells or tandem solar cells are likely to have better environmental profiles than conventional silicon based and thin film solar cells, in terms of energy consumption, greenhouse gas emissions and material consumption. However, the emerging solar cells may utilize toxic materials in which their eco-toxicity and human toxicity should be further considered during the design of the technologies. Moreover, it is identified that the energy and environmental hotspot lies in the manufacturing process, regardless of impact indicators and types of solar cells

Life Cycle Environmental Impacts and Health Effects of Protein-Rich Food as Meat Alternatives: A Review

The food sector is responsible for a considerable impact on the environment in most environmental contexts: the food supply chain causes greenhouse gas emissions, water consumption, reduction in cultivable land, and other environmental impacts. Thus, a change in food supply is required to reduce the environmental impacts caused by the food supply chain and to meet the increasing demand for sufficient and qualitative nutrition. Large herds of livestock are inappropriate to achieve these goals due to the relevant impact of meat supply chain on the environment, e.g., the land used to grow feed for animals is eight times more than that for human nutrition. The search for meat alternatives, especially for the intake of critical nutrients such as protein, is a consequent step. In the above context, this paper summarizes the health aspects of protein-rich food alternatives to meat and carries out a literature review on the life-cycle environmental impacts of this alternative food

Integrated hybrid multi-regional input-output for assessing life cycle air emissions of the Italian power system

The air emissions of the Italian power system, as well as national emissions between 2010 and 2017 and projections to 2040, have been assessed from a lifecycle perspective, using an integrated hybrid two-region input-output model of Italy versus the rest of the world. The Italian economy is divided into 42 sectors, including electricity, which is further disaggregated into seven technologies. Detailed electricity sector data, from Istat, are fed into the EXIOBASE input-output database. NAMEA tables represent overall air emissions, while the Ecoinvent database is used for the electricity sector. Electricity transition scenarios from Terna and Snam have been integrated into input-output and air emission databases. Demand and emissions were tracked within the electricity sector over medium-term, and the findings showed a sharp decrease between 2017 and 2025, from 97.5 MtCO2 to 32.6 MtCO2. By 2040, air emissions from the electricity sector are expected to grow gradually, compared to those of 2030, from 22.2 MtCO2 to 25.9 MtCO2, suggesting that the demand between 2030 and 2040 grows faster than the decarbonization effort during the same period. There is an overall, gradual downtrend between 2010 and 2040, with all air emission categories declining by half from both production and consumption-based perspectives in this period

Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds.

Salmonella enterica serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over time. These findings have general applicability to outbreak detection of bacterial pathogens

Bit-Vector Model Counting using Statistical Estimation

Approximate model counting for bit-vector SMT formulas (generalizing \#SAT) has many applications such as probabilistic inference and quantitative information-flow security, but it is computationally difficult. Adding random parity constraints (XOR streamlining) and then checking satisfiability is an effective approximation technique, but it requires a prior hypothesis about the model count to produce useful results. We propose an approach inspired by statistical estimation to continually refine a probabilistic estimate of the model count for a formula, so that each XOR-streamlined query yields as much information as possible. We implement this approach, with an approximate probability model, as a wrapper around an off-the-shelf SMT solver or SAT solver. Experimental results show that the implementation is faster than the most similar previous approaches which used simpler refinement strategies. The technique also lets us model count formulas over floating-point constraints, which we demonstrate with an application to a vulnerability in differential privacy mechanisms

A one-step, one-pot CRISPR nucleic acid detection platform (CRISPR-top): Application for the diagnosis of COVID-19.

The existing CRISPR-mediated diagnostic tests require a two-step procedure (DNA or RNA amplification followed by CRISPR-mediated sequence-specific detection) for nucleic acid detection, which increases complexity and the risk of sample cross-contamination. Here, we report a new CRISPR-mediated test, called CRISPR-top (CRISPR-mediated testing in one-pot), which integrates simultaneous target pre-amplification with CRISPR/cas12b-mediated detection into a one-pot reaction mixture, performed at a constant temperature. The novel CRISPR-top assay was applied to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19 (coronavirus disease 2019). COVID-19 CRISPR-top targets the ORF1ab (opening reading frame 1a/b) and NP (nucleoprotein) genes of SARS-CoV-2, and operates at 59 °C for 40 min with minimal instrument. The COVID-19 CRISPR-top assay can return results within 60-min and is easily interpreted by visual fluorescence or lateral flow readouts. The analytical limit of detection (LoD) for COVID-19 CRISPR-top is 10 copies (for each detection target) per reaction with no cross-reactivity observed from non-SARS-CoV-2 templates. Among clinically collected non-COVID-19 samples, the assay's specificity was 100% (80/80 oropharynx swab samples). Among 52 COVID-19 positive clinical samples collected, the COVID-19 CRISPR-top assay yielded 38 (73.1%) positive results using fluorescence readout and 35 (67.3%) positive results with lateral-flow readout. These diagnostic results were similar to those obtained using RT-PCR (34 positive (65.4%)). These data indicate that COVID-19 CRISPR-top is a simple, rapid, accurate and highly sensitive method for SARS-CoV-2 detection which can be used in the clinic, field laboratories and primary care facilities in resource-challenged settings

Enhancing Optical Up-Conversion Through Electrodynamic Coupling with Ancillary Chromophores

In lanthanide-based optical materials, control over the relevant operating characteristics–for example transmission wavelength, phase and quantum efficiency–is generally achieved through the modification of parameters such as dopant/host combination, chromophore concentration and lattice structure. An alternative avenue for the control of optical response is through the introduction of secondary, codoped chromophores. Here, such secondary centers act as mediators, commonly bridging the transfer of energy between primary absorbers of externally sourced optical input and other sites of frequency-converted emission. Utilizing theoretical models based on experimentally feasible, three-dimensional crystal lattice structures; a fully quantized theoretical framework provides insights into the locally modified mechanisms that can be implemented within such systems. This leads to a discussion of how such effects might be deployed to either enhance, or potentially diminish, the efficiency of frequency up-conversion

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation