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Almost 15 years ago, the results of the Preexposure Prophylaxis Initiative (iPrEx) trial, which showed the efficacy of oral antiretroviral agents as preexposure prophylaxis (PrEP), were reported in the Journal . 1 However, only 15% of persons who would benefit from PrEP currently receive it. 2 The recent modest fall in the global incidence of human immunodeficiency virus (HIV) infection obscures the ongoing epidemic among key populations in high-income, middle-income, and low-income countries, including continued high infection rates among young women in southern Africa. The United Nations 2030 prevention targets will not be met unless something different is done, and soon. The results . . .

Cancer cells rely on telomerase or the alternative lengthening of telomeres (ALT) pathway to overcome replicative mortality. ALT is mediated by recombination and is prevalent in a subset of human cancers, yet whether it can be exploited therapeutically remains unknown. Loss of the chromatin-remodeling protein ATRX associates with ALT in cancers. Here, we show that ATRX loss compromises cell-cycle regulation of the telomeric noncoding RNA TERRA and leads to persistent association of replication protein A (RPA) with telomeres after DNA replication, creating a recombinogenic nucleoprotein structure. Inhibition of the protein kinase ATR, a critical regulator of recombination recruited by RPA, disrupts ALT and triggers chromosome fragmentation and apoptosis in ALT cells. The cell death induced by ATR inhibitors is highly selective for cancer cells that rely on ALT, suggesting that such inhibitors may be useful for treatment of ALT-positive cancers.

Correcting errors in real time is essential for reliable large-scale quantum computations. Realizing this high-level function requires a system capable of several low-level primitives, including single-qubit and two-qubit operations, midcircuit measurements of subsets of qubits, real-time processing of measurement outcomes, and the ability to condition subsequent gate operations on those measurements. In this work, we use a 10-qubit quantum charge-coupled device trapped-ion quantum computer to encode a single logical qubit using the [[7,1,3]] color code, first proposed by Steane [Phys. Rev. Lett. 77, 793 (1996)PRLTAO0031-900710.1103/PhysRevLett.77.793]. The logical qubit is initialized into the eigenstates of three mutually unbiased bases using an encoding circuit, and we measure an average logical state preparation and measurement (SPAM) error of 1.7(2)×10⁻3, compared to the average physical SPAM error 2.4(4)×10⁻3 of our qubits. We then perform multiple syndrome measurements on the encoded qubit, using a real-time decoder to determine any necessary corrections that are done either as software updates to the Pauli frame or as physically applied gates. Moreover, these procedures are done repeatedly while maintaining coherence, demonstrating a dynamically protected logical qubit memory. Additionally, we demonstrate non-Clifford qubit operations by encoding a T[over ¯]|+⟩_(L) magic state with an error rate below the threshold required for magic state distillation. Finally, we present system-level simulations that allow us to identify key hardware upgrades that may enable the system to reach the pseudothreshold.

Operational research is required to design delivery of pre-exposure prophylaxis (PrEP) and early antiretroviral treatment (ART). This paper presents the primary analysis of programmatic data, as well as demographic, behavioural, and clinical data, from the TAPS Demonstration Project, which offered both interventions to female sex workers (FSWs) at 2 urban clinic sites in South Africa. The TAPS study was conducted between 30 March 2015 and 30 June 2017, with the enrolment period ending on 31 July 2016. TAPS was a prospective observational cohort study with 2 groups receiving interventions delivered in existing service settings: (1) PrEP as part of combination prevention for HIV-negative FSWs and (2) early ART for HIV-positive FSWs. The main outcome was programme retention at 12 months of follow-up. Of the 947 FSWs initially seen in clinic, 692 were HIV tested. HIV prevalence was 49%. Among those returning to clinic after HIV testing and clinical screening, 93% of the women who were HIV-negative were confirmed as clinically eligible for PrEP (n = 224/241), and 41% (n = 110/270) of the women who were HIV-positive had CD4 counts within National Department of Health ART initiation guidelines at assessment. Of the remaining women who were HIV-positive, 93% were eligible for early ART (n = 148/160). From those eligible, 98% (n = 219/224) and 94% (n = 139/148) took up PrEP and early ART, respectively. At baseline, a substantial fraction of women had a steady partner, worked in brothels, and were born in Zimbabwe. Of those enrolled, 22% on PrEP (n = 49/219) and 60% on early ART (n = 83/139) were seen at 12 months; we observed high rates of loss to follow-up: 71% (n = 156/219) and 30% (n = 42/139) in the PrEP and early ART groups, respectively. Little change over time was reported in consistent condom use or the number of sexual partners in the last 7 days, with high levels of consistent condom use with clients and low use with steady partners in both study groups. There were no seroconversions on PrEP and 7 virological failures on early ART among women remaining in the study. Reported adherence to PrEP varied over time between 70% and 85%, whereas over 90% of participants reported taking pills daily while on early ART. Data on provider-side costs were also collected and analysed. The total cost of service delivery was approximately US$126 for PrEP and US$406 for early ART per person-year. The main limitations of this study include the lack of a control group, which was not included due to ethical considerations; clinical study requirements imposed when PrEP was not approved through the regulatory system, which could have affected uptake; and the timing of the implementation of a national sex worker HIV programme, which could have also affected uptake and retention. PrEP and early ART services can be implemented within FSW routine services in high prevalence, urban settings. We observed good uptake for both PrEP and early ART; however, retention rates for PrEP were low. Retention rates for early ART were similar to retention rates for the current standard of care. While the cost of the interventions was higher than previously published, there is potential for cost reduction at scale. The TAPS Demonstration Project results provided the basis for the first government PrEP and early ART guidelines and the rollout of the national sex worker HIV programme in South Africa.

Infant birth weight affects neuromotor and biomechanical swallowing performance in infant pig models. Preterm infants are generally born low birth weight and suffer from delayed development and neuromotor deficits. These deficits include critical life skills such as swallowing and breathing. It is unclear whether these neuromotor and biomechanical deficits are a result of low birth weight or preterm birth. In this study we ask: are preterm infants simply low birth weight infants or do preterm infants differ from term infants in weight gain and swallowing behaviors independent of birth weight? We use a validated infant pig model to show that preterm and term infants gain weight differently and that birth weight is not a strong predictor of functional deficits in preterm infant swallowing. We found that preterm infants gained weight at a faster rate than term infants and with nearly three times the variation. Additionally, we found that the number of sucks per swallow, swallow duration, and the delay of the swallows relative to the suck cycles were not impacted by birth weight. These results suggest that any correlation of developmental or swallowing deficits with reduced birth weight are likely linked to underlying physiological immaturity of the preterm infant.

Pneumocystis jirovecii is an opportunistic fungal pathogen responsible for Pneumocystis pneumonia (PCP) in immunocompromised patients. Antifolate drugs targeting the dihydrofolate reductase (DHFR), including trimethoprim (TMP), remain central to treatment, but studying the effects of mutations in DHFR on resistance to treatment is limited by our inability to culture this organism in vitro or in animal models. We expressed P. jirovecii DHFR (PjDHFR) in Saccharomyces cerevisiae and performed deep mutational scanning (DMS) on this protein to measure the effects of all single amino-acid substitutions on enzyme function and resistance to methotrexate (MTX), a model antifolate which shares structural features with TMP. We integrated experimental results with structural and evolutionary features from multiple biophysical modeling approaches, and by using an interpretable machine-learning framework, we trained a random forest model to classify MTX resistance-conferring mutations in PjDHFR. We then leveraged this framework as a prediction tool to model the effects of mutations on resistance to TMP, which cannot be directly assayed experimentally. Functional measurements from DMS were the strongest contributors to resistance prediction and generally outperformed purely computational features. Resistance-conferring mutations were constrained by function, revealing a functional-resistance trade-off within this essential protein. Feature contribution analyses highlighted key predictors such as distance to ligand, flexibility, stability, and functional trade-off as determinants of resistance. When extrapolated to TMP, the model identified candidate resistance mutations consistent with known biochemical constraints of DHFR. We demonstrate how experimentally measured functional landscapes can be combined with biophysical modeling to help understand and predict antifolate resistance in an unculturable fungal pathogen. Our results provide biological insight into the constraints affecting the evolution of resistance in PjDHFR, and support that resistance arises from mutations altering drug interactions while preserving function. We illustrate how DMS data can enable generalizable, mechanistically interpretable models of drug resistance across structurally related antifolates.

Pneumocystis jirovecii is a fungal pathogen that causes pneumocystis pneumonia, a disease that mainly affects immunocompromised individuals. This fungus has historically been hard to study because of our inability to grow it in vitro . One of the main drug targets in P . jirovecii is its dihydrofolate reductase (PjDHFR). Here, by using functional complementation of the baker’s yeast ortholog, we show that PjDHFR can be inhibited by the antifolate methotrexate in a dose-dependent manner. Using deep mutational scanning of PjDHFR, we identify mutations conferring resistance to methotrexate. Thirty-one sites spanning the protein have at least one mutation that leads to resistance, for a total of 355 high-confidence resistance mutations. Most resistance-inducing mutations are found inside the active site, and many are structurally equivalent to mutations known to lead to resistance to different antifolates in other organisms. Some sites show specific resistance mutations, where only a single substitution confers resistance, whereas others are more permissive, as several substitutions at these sites confer resistance. Surprisingly, one of the permissive sites (F199) is without direct contact to either ligand or cofactor, suggesting that it acts through an allosteric mechanism. Modeling changes in binding energy between F199 mutants and drug shows that most mutations destabilize interactions between the protein and the drug. This evidence points towards a more important role of this position in resistance than previously estimated and highlights potential unknown allosteric mechanisms of resistance to antifolate in DHFRs. Our results offer unprecedented resources for the interpretation of mutation effects in the main drug target of an uncultivable fungal pathogen.

BackgroundThe formation of a bolus of food is critical for proper feeding function, and there is substantial variation in the size and shape of a bolus prior to a swallow. Preterm infants exhibit decreased abilities to acquire and process food, but how that relates to their bolus size and shape is unknown. Here, we test two hypotheses: (1) that bolus size and shape will differ between term and preterm infants, and (2) bolus size and shape will change longitudinally through development in both term and preterm infants.MethodsTo test these hypotheses, we measured bolus size and shape in preterm and term infant pigs longitudinally through nursing using high-speed videofluoroscopy.ResultsPreterm infant pigs swallowed smaller volumes of milk. Although term infants increased the amount of milk per swallow as they aged, preterm infants did not. These changes in bolus volume were also correlated with changes in bolus shape; larger boluses became more elongate as they better filled the available anatomical space of the valleculae.ConclusionsThese results suggest that preterm birth reduces the ability of preterm pigs to increase bolus size as they grow, affecting development in this fragile population. These results highlight that studies on term infant feeding may not translate to preterm infants.

Feeding difficulties are especially prevalent in preterm infants, although the mechanisms driving these difficulties are poorly understood due to a lack of data on healthy infants. One potential mechanism of dysphagia in adults is correlated with bolus volume. Yet, whether and how bolus volume impacts swallow safety in infant feeding is unknown. A further complication for safe infant swallowing is recurrent laryngeal nerve (RLN) injury due to patent ductus arteriosus surgery, which exacerbates the issues that preterm infants face and can increase the risk of dysphagia. Here, we used a validated animal model feeding freely to test the effect of preterm birth, postnatal maturation and RLN lesion and their interactions on swallow safety. We also tested whether bolus size differed with lesion or birth status, and the relationship between bolus size and swallow safety. We found very little effect of lesion on swallow safety, and preterm infants did not experience more penetration or aspiration than term infants. However, term infants swallowed larger boluses than preterm infants, even after correcting for body size. Bolus size was the primary predictor of penetration or aspiration, with larger boluses being more likely to result in greater degrees of dysphagia irrespective of age or lesion status. These results highlight that penetration and aspiration are likely normal occurrences in infant feeding. Further, when comorbidities, such as RLN lesion or preterm birth are present, limiting bolus size may be an effective means to reduce incidences of penetration and aspiration.

Movements of the hyoid and thyroid are critical for feeding. These structures are often assumed to move in synchrony, despite evidence that neurologically compromised populations exhibit altered kinematics. Preterm infants are widely considered to be a neurologically compromised population and often experience feeding difficulties, yet measuring performance, and how performance matures in pediatric populations is challenging. Feeding problems are often compounded by complications arising from surgical procedures performed to ensure the survival of preterm infants, such as damage to the recurrent laryngeal nerve (RLN) during patent ductus arteriosus correction surgery. Here, we used a validated infant pig model for infant feeding to test how preterm birth, postnatal maturation, and RLN lesion interact to impact hyoid and thyroid excursion and their coordination. We filmed infant pigs when feeding using videofluorscopy at seven days old (1–2 months human equivalent) and 17 days old (6–9 months human equivalent) and tracked movements of the hyoid and thyroid on both days. We found that preterm birth impacted the coordination between hyoid and thyroid movements, but not their actual excursion. In contrast, excursion of the two structures increased with postnatal age in term and preterm pigs. RLN lesion decreased thyroid excursion, and primarily impacted hyoid movements by increasing variation in hyoid excursion. This work demonstrates that RLN lesion and preterm birth have distinct, but pervasive effects on feeding performance in infants, and suggest that interventions targeted towards reducing dysphagia should be prescribed based off the etiology driving dysphagia, rather than the prognosis of dysphagia.