Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on short tandem repeat sequence nomenclature.

The DNA Commission of the International Society for Forensic Genetics (ISFG) has developed a set of nomenclature recommendations for short tandem repeat (STR) sequences. These recommendations follow the 2016 considerations of the DNA Commission of the ISFG, incorporating the knowledge gained through research and population studies in the intervening years. While maintaining a focus on backward compatibility with the CE data that currently populate national DNA databases, this report also looks to the future with the establishment of recommended minimum sequence reporting ranges to facilitate interlaboratory comparisons, automated solutions for sequence-based allele designations, a suite of resources to support bioinformatic development, guidance for characterizing new STR loci, and considerations for incorporating STR sequences and other new markers into investigative databases.

A Functional Restoration Program for Active Duty Service Members With Chronic Pain: Examining the Impact of Co-occurring PTSD on Treatment Response.

INTRODUCTION: Standard medical intervention for chronic pain may be less effective in the presence of co-occurring PTSD. Functional restoration programs (FRPs), which combine psychological interventions and progressive exercise rehabilitation, represent an alternative to standard medical intervention for chronic pain. The objective of the current study is to evaluate a FRP serving Active Duty Service Members with chronic pain and to examine whether co-occurring PTSD symptoms are associated with differential treatment response. METHODS: This is a retrospective observational study of data previously collected at Naval Medical Center San Diego approved by the Naval Medical Center San Diego Institutional Review Board. The study included 81 Active Duty Service Members, primarily Sailors and Marines, who completed a FRP, and examined pre- to post-treatment changes in Pain Impact Score-a composite measure of pain intensity, pain interference, and physical functioning-as well as measures of mental health and pain cognitions. Co-occurring PTSD symptoms were examined as a potential moderator of treatment response. RESULTS: Twenty-three patients (28.4%) screened positive for PTSD during baseline assessments. Repeated measures analysis of variance showed statistically significant improvement in Pain Impact Score for the full sample (P <.001). Although no significant interactions with probable PTSD were demonstrated for measures of pain intensity and physical functioning (both Ps >.05), patients screening positive for PTSD demonstrated a lesser decrease in pain interference compared to patients screening negative for PTSD (P <.01). Improvements in measures of mental health and pain cognitions were also statistically significant for the full sample (all P values <.05) and did not differ as a function of PTSD symptoms (all P values >.05). CONCLUSION: This FRP primarily serving Sailors and Marines contributed to broad overall improvements in the domains of pain and functioning as well as mental health and pain cognitions. Co-occurring PTSD symptoms were not associated with poorer treatment response on most measured outcomes.

THz-TDS with gigahertz Yb-based dual-comb lasers: noise analysis and mitigation strategies.

We investigate terahertz time-domain spectroscopy using a low-noise dual-frequency-comb laser based on a single spatially multiplexed laser cavity. The laser cavity includes a reflective biprism, which enables generation of a pair of modelocked output pulse trains with slightly different repetition rates and highly correlated noise characteristics. These two pulse trains are used to generate the THz waves and detect them by equivalent time sampling. The laser is based on Yb:CALGO, operates at a nominal repetition rate of 1.18 GHz, and produces 110 mW per comb with 77 fs pulses around 1057 nm. We perform THz measurements with Fe-doped photoconductive antennas, operating these devices with gigahertz 1 µm lasers for the first time, to our knowledge, and obtain THz signal currents approximately as strong as those from reference measurements at 1.55 µm and 80 MHz. We investigate the influence of the laser's timing noise properties on THz measurements, showing that the laser's timing jitter is quantitatively explained by power-dependent shifts in center wavelength. We demonstrate reduction in noise by simple stabilization of the pump power and show up to 20 dB suppression in noise by the combination of shared pumping and shared cavity architecture. The laser's ultra-low-noise properties enable averaging of the THz waveform for repetition rate differences from 1 kHz to 22 kHz, resulting in a dynamic range of 55 dB when operating at 1 kHz and averaging for 2 s. We show that the obtained dynamic range is competitive and can be well explained by accounting for the measured optical delay range, integration time, as well as the measurement bandwidth dependence of the noise from transimpedance amplification. These results will help enable a new approach to high-resolution THz-TDS enabled by low-noise gigahertz dual-comb lasers.

Scan-less 3D microscopy based on spatiotemporal encoding on a single-cavity dual-comb laser.

Dual-comb microscopy enables high-speed and high-precision optical sampling by simultaneously extracting both amplitude and phase information from the interference signals with frequency division multiplexing. In this Letter, we introduce a spatiotemporal encoding approach for dual-comb microscopy that overcomes previous limitations such as mechanical scanning, low sampling efficiency, and system complexity. By employing free-space angular-chirp-enhanced delay (FACED) and a low-noise single-cavity dual-comb laser, we achieve scan-less 3D imaging with nanometer precision and a 3D distance-imaging rate of 330 Hz, restricted only by the repetition rate difference of the dual-comb laser. Specifically, the FACED unit linearly arranges the laser beam into an array. A grating subsequently disperses this array transversely into lines, facilitating ultrafast spectroscopic applications that are 1-2 orders of magnitude quicker than traditional dual-comb methods. This spatiotemporal encoding also eases the stringent conditions on various dual-comb laser parameters, such as repetition rates, coherence, and stability. Through carefully designed experiments, we demonstrate that our scan-less system can measure 3D profiles of microfabricated structures at a rate of 7 million pixels per second. Our method significantly enhances measurement speed while maintaining high precision, using a compact light source. This advancement has the potential for broad applications, including phase imaging, surface topography, distance ranging, and spectroscopy.

Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders.

Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.

Harmonizing the forensic nomenclature for STR loci D6S474 and DYS612.

The autosomal STR D6S474 and the Y-chromosomal STR DYS612 have been reported in multiple ways in the forensic literature, with differences in both the bracketed repeat structures and counting of numerical length-based capillary electrophoresis (CE) alleles. These issues often come to light when STR loci are introduced in commercial assays and results compared with historical publications of allele frequency data, or multiple assays are characterized with reference materials. We review the forensic literature and other relevant information, and provide suggestions for the future treatment of each STR.

Mental Health Predictors of Response to Standard Medical Intervention at a Military Pain Specialty Clinic.

INTRODUCTION: Chronic pain among active duty service members can negatively impact operational readiness and contributes to significant health care costs within military treatment facilities. Response to standard medical intervention (SMI) for chronic pain is highly variable. The objective of the current study was to examine whether mental health indicators predict individual variation in response to SMI for chronic pain in a military pain specialty clinic. METHODS: This is a retrospective observational study of data previously collected at the Pain Medicine Center at Naval Medical Center San Diego (NMCSD) approved by the NMCSD Institutional Review Board. We included 286 ADSMs who completed the Pain Assessment Screening Tool and Outcomes Registry (PASTOR) at two assessment points (mean = 118.45 days apart, SD = 37.22) as part of standard care. Hierarchical linear regression analyses were conducted to examine whether pretreatment mental health measures predict changes in the pain impact score (PIS)-a composite measure of pain intensity, pain interference, and physical functioning-over the course of treatment. RESULTS: After controlling for pretreatment PIS, pretreatment PTSD symptoms, fatigue, and anger were all significant predictors of posttreatment PIS: Higher PTSD symptoms, higher fatigue, and lower anger predicted poorer response to treatment (all Ps < .05). CONCLUSION: Higher pretreatment PTSD and fatigue symptoms may portend poorer response to SMI for chronic pain. Poor response to treatment may also be predicted by lower pretreatment anger. Further investigation is warranted to identify the best strategies for treating chronic pain in military treatment facilities when these conditions are identified during initial evaluation.

Ultrafast Yb:YAG laser oscillator with gigahertz repetition rate.

We present a SESAM modelocked Yb:YAG solid-state laser providing low-noise narrowband pulses with a pulse duration of 606 fs at a 1.09-GHz repetition rate, delivering up to 2.5 W of average output power. This laser provides access to a new parameter space that could previously not be reached by solid-state lasers and, to the best of our knowledge, is the first modelocked solid-state Yb:YAG laser in the gigahertz regime. This is achieved by introducing a single additional intracavity element, specifically a nonlinear birefringent YVO4 crystal, for soliton formation, polarization selection, and cavity intensity clamping. The isotropic pump absorption in Yb:YAG allows for stable and low-noise operation with multimode fiber pumping. This laser is ideally suited as a seed source for many commercial high-power Yb-doped amplification systems operating at a center wavelength around 1.03 µm. The laser exhibits a high power per comb line of 5.0 mW which also makes it interesting for applications in frequency comb spectroscopy, especially if it is used to pump an optical parametric oscillator. We measure a relative intensity noise (RIN) of 0.03%, integrated from 1 Hz to 10 MHz. Furthermore, we show that the laser timing jitter for noise frequencies >2 kHz is fully explained by a power-dependent shift in the center wavelength of 0.38 nm/W due to the quasi-three-level laser gain material. The narrow gain bandwidth of Yb:YAG reduces this contribution to noise in comparison to other SESAM modelocked Yb-doped lasers.

Discovery of AZD4747, a Potent and Selective Inhibitor of Mutant GTPase KRASG12C with Demonstrable CNS Penetration.

The glycine to cysteine mutation at codon 12 of Kirsten rat sarcoma (KRAS) represents an Achilles heel that has now rendered this important GTPase druggable. Herein, we report our structure-based drug design approach that led to the identification of 14, AZD4747, a clinical development candidate for the treatment of KRASG12C-positive tumors, including the treatment of central nervous system (CNS) metastases. Building on our earlier discovery of C5-tethered quinazoline AZD4625, excision of a usually critical pyrimidine ring yielded a weak but brain-penetrant start point which was optimized for potency and DMPK. Key design principles and measured parameters that give high confidence in CNS exposure are discussed. During optimization, divergence between rodent and non-rodent species was observed in CNS exposure, with primate PET studies ultimately giving high confidence in the expected translation to patients. AZD4747 is a highly potent and selective inhibitor of KRASG12C with an anticipated low clearance and high oral bioavailability profile in humans.

The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes.

Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.

Discovery and Optimization of the First ATP Competitive Type-III c-MET Inhibitor.

Recent clinical reports have highlighted the need for wild-type (WT) and mutant dual inhibitors of c-MET kinase for the treatment of cancer. We report herein a novel chemical series of ATP competitive type-III inhibitors of WT and D1228V mutant c-MET. Using a combination of structure-based drug design and computational analyses, ligand 2 was optimized to a highly selective chemical series with nanomolar activities in biochemical and cellular settings. Representatives of the series demonstrate excellent pharmacokinetic profiles in rat in vivo studies with promising free-brain exposures, paving the way for the design of brain permeable drugs for the treatment of c-MET driven cancers.

Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age.

Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.

Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference.

Biogeographical ancestry (BGA) inference from ancestry-informative markers (AIMs) has strong potential to support forensic investigations. Over the past two decades, several forensic panels composed of AIMs have been developed to predict ancestry at a continental scale. These panels typically comprise fewer than 200 AIMs and have been designed and tested with a limited set of populations. How well these panels recover patterns of genetic diversity relative to larger sets of markers, and how accurately they infer ancestry of individuals and populations not included in their design remains poorly understood. The lack of comparative studies addressing these aspects makes the selection of appropriate panels for forensic laboratories difficult. In this study, the model-based genetic clustering tool STRUCTURE was used to compare three popular forensic BGA panels: MAPlex, Precision ID Ancestry Panel (PIDAP), and VISAGE Basic Tool (VISAGE BT) relative to a genome-wide reference set of 10k SNPs. The genotypes for all these markers were obtained for a comprehensive set of 3957 individuals from 228 worldwide human populations. Our results indicate that at the broad continental scale (K=6) typically examined in forensic studies, all forensic panels produced similar genetic structure patterns compared to the reference set (G'≈90%) and had high classification performance across all regions (average AUC-PR > 97%). However, at K= 7 and K= 8, the forensic panels displayed some region-specific clustering deviations from the reference set, particularly in Europe and the region of East and South-East Asia, which may be attributed to differences in the design of the respective panels. Overall, the panel with the most consistent performance in all regions was VISAGE BT with an average weighted AUC̅W score of 96.26% across the three scales of geographical resolution investigated.

Gene Expression and Pathway Analysis in Rat Brain and Liver After Exposure to Royal Demolition Explosive (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine).

The nitramine explosive, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is associated with acute and chronic toxicity in mammals and targets both the central nervous system and liver. After a single oral dose of RDX in male rats, the systemic distribution of RDX and the toxicodynamic response was measured using clinical chemistry and Affymetrix Rat Genome® 230 2.0 gene expression arrays, respectively. Nominal doses of 0, 9 and 36 mg/kg pure RDX were administered to animals followed by liver, cerebral cortex, and hippocampus gene expression analysis at 0, 3.5, 24, and 48 hours. RDX quickly entered the liver and brain, increasing up to 24 hours. For the 36 mg/kg dose, RDX was still measurable in liver and brain at 48 hours, but was non-detectible for the 9 mg/kg dose. At 3.5 hours, the time within which most convulsions reportedly occur after RDX ingestion, the hippocampus displayed the highest response for both gene expression and pathways, while the cortex was relatively non-responsive. The top 2 impacted pathways, primarily involved in neurotransmission, were the GABAergic and glutamatergic pathways. High numbers of genes also responded to RDX in the liver with P450 metabolism pathways significantly involved. Compared to the liver, the hippocampus displayed more consistent biological effects across dose and time with neurotransmission pathways predominating. Overall, based on gene expression data, RDX responses were high in both the hippocampus and liver, but were minimal in the cerebral cortex. These results identify the hippocampus as an important target for RDX based on gene expression.

Single-cavity dual-modelocked 2.36-µm laser.

We present the first dual-modelocked femtosecond oscillator operating beyond 2 µm wavelength. This new class of laser is based on a Cr:ZnS gain medium, an InGaSb SESAM for modelocking, and a two-surface reflective device for spatial duplexing of the two modelocked pulse trains (combs). The laser operates at 2.36 µm, and for each comb, we have achieved a FWHM spectral bandwidth of 30 nm, an average power of over 200 mW, and a pulse duration close to 200 fs. The nominal repetition rate is 242 MHz with a sufficiently large repetition rate difference of 4.17 kHz. We also found that the laser is able to produce stable modelocked pulses over a wide range of output powers. This result represents a significant step towards realizing dual-comb applications directly above 2 µm using a single free-running laser.

Free-running Yb:KYW dual-comb oscillator in a MOPA architecture.

Single-cavity dual-combs comprise a rapidly emerging technology platform suitable for a wide range of applications like optical ranging, equivalent time sampling, and spectroscopy. However, it remains a challenging task to develop a dual-comb system that exhibits low relative frequency fluctuations to allow for comb line resolved measurements, while simultaneously offering high average power and short pulse durations. Here we combine a passively cooled and compact dual-comb solid-state oscillator with a pair of core-pumped Yb-fiber-based amplifiers in a master-oscillator power-amplifier (MOPA) architecture. The Yb:KYW oscillator operates at 250 MHz and uses polarization multiplexing for dual-comb generation. To the best of our knowledge, this is the first demonstration of a single-cavity dual-comb based on this gain material. As the pulse timing characteristics inherent to the oscillator are preserved in the amplification process, the proposed hybrid approach leverages the benefit of both the ultra-low noise solid-state laser and the advantages inherent to fiber amplifier systems such as straight-forward power scaling. The amplifier is optimized for minimal pulse broadening while still providing significant amplification and spectral broadening. We obtain around 1 W of power per output beam with pulses then compressed down to sub-90 fs using a simple grating compressor, while no pre-chirping or other dispersion management is needed. The full-width half-maximum (FWHM) of the radio-frequency comb teeth is 700 Hz for a measurement duration of 100 ms, which is much less than the typical repetition rate difference, making this passively stable source well-suited for indefinite coherent signal averaging via computational phase tracking.

Isotropization of a Rotating and Longitudinally Expanding ϕ4 Scalar System.

We study numerically the evolution of an expanding system of scalar fields. The initial configuration is non-isotropic and rotating. We calculate the energy-momentum tensor and angular momentum vector of the system. We compare the time scales associated with the isotropization of the transverse and longitudinal pressures, and the decay of the initial angular momentum. We show that even a fairly large initial angular momentum decays significantly faster than the pressure anisotropy.

Influence of disk aberrations on high-power thin-disk laser cavities.

We present a systematic study on the influence of thin-disk aberrations on the performance of thin-disk laser oscillators. To evaluate these effects, we have developed a spatially resolved numerical model supporting arbitrary phase profiles on the intracavity components that estimates the intracavity beam shape and the output power of thin-disk laser oscillators. By combining this model with the experimentally determined phase profile of the thin-disk (measured with interferometry), we can predict the operation mode of high-power thin-disk lasers, including mode degradation, higher-order mode coupling, and stability zone shrinking, all of which are in good agreement with experiment. Our results show that one of the main mechanisms limiting the performance is the small deviation of the disk's phase profile from perfect radial symmetry. This result is an important step to scaling modelocked thin-disk oscillators to the kW-level and will be important in the design of future active multi-pass cavity arrangements.

Dynamic and precise long-distance ranging using a free-running dual-comb laser.

Long-distance ranging is a crucial tool for both industrial and scientific applications. Laser-based distance metrology offers unprecedented precision making it the ideal approach for many deployments. In particular, dual-comb ranging is favorable due to its inherently high precision and sampling rate. To make high-performance long-range dual-comb LiDAR more accessible by reducing both cost and complexity, here we demonstrate a fiber-based dual-comb LiDAR frontend combined with a free-running diode-pumped solid-state dual-comb laser that allows for sub-µm measurement precision while offering a theoretical ambiguity range of more than 200 km. Our system simultaneously measures distance with the role of each comb interchanged, thereby enabling Vernier-based determination of the number of ambiguity ranges. As a proof-of-principle experiment, we measure the distance to a moving target over more than 10 m with sub-µm precision and high update rate, corresponding to a relative precision of 10-7. For a static target at a similar distance, we achieve an instantaneous precision of 0.29 µm with an update time of 1.50 ms. With a longer averaging time of 200 ms, we reach a precision of around 33 nm, which corresponds to a relative precision of about 3·10-9 with a time-of-flight-based approach.

Discovery of AZD4625, a Covalent Allosteric Inhibitor of the Mutant GTPase KRASG12C.

KRAS is an archetypal high-value intractable oncology drug target. The glycine to cysteine mutation at codon 12 represents an Achilles heel that has now rendered this important GTPase druggable. Herein, we report our structure-based drug design approach that led to the identification of 21, AZD4625, a clinical development candidate for the treatment of KRASG12C positive tumors. Highlights include a quinazoline tethering strategy to lock out a bio-relevant binding conformation and an optimization strategy focused on the reduction of extrahepatic clearance mechanisms seen in preclinical species. Crystallographic analysis was also key in helping to rationalize unusual structure-activity relationship in terms of ring size and enantio-preference. AZD4625 is a highly potent and selective inhibitor of KRASG12C with an anticipated low clearance and high oral bioavailability profile in humans.