The Mason-Alberta Phonetic Segmenter: A forced alignment system based on deep neural networks and interpolation

Forced alignment systems automatically determine boundaries between segments in speech data, given an orthographic transcription. These tools are commonplace in phonetics to facilitate the use of speech data that would be infeasible to manually transcribe and segment. In the present paper, we describe a new neural network-based forced alignment system, the Mason-Alberta Phonetic Segmenter (MAPS). The MAPS aligner serves as a testbed for two possible improvements we pursue for forced alignment systems. The first is treating the acoustic model in a forced aligner as a tagging task, rather than a classification task, motivated by the common understanding that segments in speech are not truly discrete and commonly overlap. The second is an interpolation technique to allow boundaries more precise than the common 10 ms limit in modern forced alignment systems. We compare configurations of our system to a state-of-the-art system, the Montreal Forced Aligner. The tagging approach did not generally yield improved results over the Montreal Forced Aligner. However, a system with the interpolation technique had a 27.92% increase relative to the Montreal Forced Aligner in the amount of boundaries within 10 ms of the target on the test set. We also reflect on the task and training process for acoustic modeling in forced alignment, highlighting how the output targets for these models do not match phoneticians' conception of similarity between phones and that reconciliation of this tension may require rethinking the task and output targets or how speech itself should be segmented.Comment: submitted for publicatio

Perception of Unfamiliar English Phonemes by Native Mandarin Speakers

In second language acquisition, speech sounds, or phonemes, not present in a learner’s native language often pose an extra challenge for speech production. When hearing one of these unfamiliar phonemes, the learner either maps it to a similar native phoneme, perceives it as a completely foreign sound, or does not perceive it as speech at all. In the first case, the learner is unable to perceive a difference between the unfamiliar phoneme and the native phoneme to which it is mapped. This mapping difficulty potentially creates problems for the learner during word recognition. The present research investigated the extent to which English phonemes absent from the Mandarin phonological inventory impact processing of native Mandarin speakers in an auditory lexical decision task. Results of this research will expand the understanding of second language perception, especially within the context of auditory lexical decision tasks. A list of ten phonemes—/ɪ/, /æ/, /ʊ/, /ɛ/, /v/, /z/, /ʒ/, /ɵ/, /ð/, /ʤ/—present in the English phonological inventory but absent from that of Mandarin were identified as unfamiliar to native Mandarin speakers. Data from the Massive Auditory Lexical Decision (MALD) database, in which participants decided whether recorded utterances were English words or made-up words, were utilized. The effects of the proportion of unfamiliar phonemes, proportion of unfamiliar vowels, and proportion of unfamiliar consonants on reaction time, representative of processing difficulty, were then calculated using statistical techniques. It was found that the proportion of all unfamiliar phonemes in an utterance had no significant effect on the reaction time of the native Mandarin speakers. However, when the list of unfamiliar phonemes was divided into vowels and consonants, a greater proportion of unfamiliar vowels was noticed to increase reaction time, while a greater proportion of unfamiliar consonants was found to decrease reaction time. Further research in this area is required to determine a concrete explanation for these results. Interestingly, when the same analysis was performed on the data of native English speakers, similar results were observed. This may reflect a common language processing mechanism in second language learners and native speakers

SWOG 1815: A phase III randomized trial of gemcitabine, cisplatin, and nab-paclitaxel versus gemcitabine and cisplatin in newly diagnosed, advanced biliary tract cancers

Background: Biliary tract cancers (BTCs) are a heterogeneous group of malignancies with a dismal prognosis. Gemcitabine-based regimens are the standard of care in advanced disease, but median overall survival (OS) is roughly 12 months. The addition of albumin-bound paclitaxel to gemcitabine and cisplatin (GAP) demonstrated promising efficacy in a 60 patient, single-arm phase II study (Shroff et al, JAMA Oncol 2019), with observed median OS of 19.2 months. Methods: SWOG 1815 is a randomized, open-label, phase III trial comparing GAP to gemcitabine/cisplatin (GC). The study included newly diagnosed advanced BTC patients (pts), randomized 2:1 to GAP vs. GC. GAP included gemcitabine at 800 mg/m2, cisplatin at 25 mg/m2 and albumin-bound paclitaxel at 100 mg/m2 on days 1 and 8 of a 21-day cycle. GC included standard dosing of gemcitabine at 1000 mg/m2 and cisplatin at 25 mg/m2 on days 1 and 8 of a 21-day cycle. Pts were treated until progression. The primary endpoint was overall survival (OS) with a target hazard ratio of 0.7 with 90% power and a 1-sided alpha of 0.025; randomization was stratified by disease site (intrahepatic cholangiocarcinoma [CCA] vs gallbladder adenocarcinoma [GBC] vs extrahepatic CCA), disease stage (locally advanced vs metastatic), and Zubrod PS 0 vs 1. Results: Of 441 eligible pts randomized, 55% were female. 67% of patients had intrahepatic CCA, 16% had GBC and 17% had extrahepatic CCA. Most pts had metastases (73%). Median OS with GAP vs. GC was 14 vs. 12.7 mo respectively (HR 0.93, 95% CI 0.74-1.19, p=0.58), ORR (confirmed and unconfirmed) 34% vs25% (p=0.11) and median PFS 8.2 vs 6.4 mo (HR 0.92, 95% CI 0.72-1.16, p=0.47), respectively. Grade 3 and 4 treatment related adverse events (TRAEs) in ≥10% of pts for GAP and GC were anemia, neutropenia, and thrombocytopenia. GAP had more ≥ grade 3 hematologic AEs compared to the GC arm (60% vs. 45%, p=0.003). Discontinuation due to toxicity was at 24% vs 19% (p=0.26) with GAP vs GC. In exploratory subset analyses, GAP vs GC improved OS in pts with locally advanced disease (medians 19.2 vs 13.7 mo; HR 0.67, 95% CI 0.42- 1.06, p=0.09) and in GBC pts (medians 17.0 vs 9.3 mo; HR 0.74, 95% CI 0.41-1.35, p=0.33). ORR for GAP vs GC in GBC was 50% vs 24% (p=0.09) and for locally advanced disease 28 vs 21% p=0.74. Conclusions: SWOG 1815 did not result in a statistically significant improvement in median OS with GAP vs. GC. The GAP regimen had higher rates of TRAEs without a statistically significant difference in discontinuation rates. Pts with locally advanced disease and GBC may benefit from the use of GAP. Further analyses are ongoing to understand potential benefit of GAP in subsets of BTC pts. Funding: NIH/National Cancer Institute grants CA180888, CA180819, CA180820, CA180821, and CA180868; and in part by Celgene Corporation, Summit, NJ (subsidiary of Bristol Myer Squibb)

The effect of collagen organization on tensile strength loss in anterior cruciate ligament grafts post-reconstruction surgery

Gemstone Team LEGSGrafts used for anterior cruciate ligament (ACL) reconstructions fall short of restoring native mechanics. This study investigated a morphological cause for tension loss by comparing native ACL and two common grafts, bone-patellar tendonbone (BPTB) and semitendinosus/gracilis hamstring tendon (ST/G), in a cadaveric system. Tension loss during continuous passive motion was quantified via force transducer. Microstructural changes were assessed by measuring collagen crimp angles. No significant differences were found for rates of percent tension loss relative to total tension loss among grafts. However, all groups displayed exponential decay, implying rapid tension loss. The crimp angles for the unstressed grafts were significantly different from each other, suggesting innate differences. The percent change experienced by stressed grafts, normalized to their unstressed baselines, showed that ST’s crimp behavior was significantly different from that of ACL and BPTB, implying the BPTB graft is superior for ACL reconstruction because it better mimics the ACL’s morphological behavior

Differential limit on the extremely-high-energy cosmic neutrino flux in the presence of astrophysical background from nine years of IceCube data

We report a quasi-differential upper limit on the extremely-high-energy (EHE) neutrino flux above $5\times 10^{6}$ GeV based on an analysis of nine years of IceCube data. The astrophysical neutrino flux measured by IceCube extends to PeV energies, and it is a background flux when searching for an independent signal flux at higher energies, such as the cosmogenic neutrino signal. We have developed a new method to place robust limits on the EHE neutrino flux in the presence of an astrophysical background, whose spectrum has yet to be understood with high precision at PeV energies. A distinct event with a deposited energy above $10^{6}$ GeV was found in the new two-year sample, in addition to the one event previously found in the seven-year EHE neutrino search. These two events represent a neutrino flux that is incompatible with predictions for a cosmogenic neutrino flux and are considered to be an astrophysical background in the current study. The obtained limit is the most stringent to date in the energy range between $5 \times 10^{6}$ and $5 \times 10^{10}$ GeV. This result constrains neutrino models predicting a three-flavor neutrino flux of $E_\nu^2\phi_{\nu_e+\nu_\mu+\nu_\tau}\simeq2\times 10^{-8}\ {\rm GeV}/{\rm cm}^2\ \sec\ {\rm sr}$at$10^9\ {\rm GeV}$. A significant part of the parameter-space for EHE neutrino production scenarios assuming a proton-dominated composition of ultra-high-energy cosmic rays is excluded.Comment: The version accepted for publication in Physical Review

Search for Kaluza-Klein Graviton Emission in ppˉp\bar{p} Collisions at s=1.8\sqrt{s}=1.8 TeV using the Missing Energy Signature

We report on a search for direct Kaluza-Klein graviton production in a data sample of 84 ${pb}^{-1}$ of \ppb collisions at $\sqrt{s}$ = 1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and one or two high energy jets. We compare the data with the predictions from a $3+1+n$-dimensional Kaluza-Klein scenario in which gravity becomes strong at the TeV scale. At 95% confidence level (C.L.) for $n$=2, 4, and 6 we exclude an effective Planck scale below 1.0, 0.77, and 0.71 TeV, respectively.Comment: Submitted to PRL, 7 pages 4 figures/Revision includes 5 figure

Measurement of the average time-integrated mixing probability of b-flavored hadrons produced at the Tevatron

We have measured the number of like-sign (LS) and opposite-sign (OS) lepton pairs arising from double semileptonic decays of $b$ and $\bar{b}$-hadrons, pair-produced at the Fermilab Tevatron collider. The data samples were collected with the Collider Detector at Fermilab (CDF) during the 1992-1995 collider run by triggering on the existence of $\mu \mu$ and $e \mu$ candidates in an event. The observed ratio of LS to OS dileptons leads to a measurement of the average time-integrated mixing probability of all produced $b$-flavored hadrons which decay weakly, $\bar{\chi} = 0.152 \pm 0.007$ (stat.) $\pm 0.011$ (syst.), that is significantly larger than the world average $\bar{\chi} = 0.118 \pm 0.005$.Comment: 47 pages, 10 figures, 15 tables Submitted to Phys. Rev.

Search for a Fourth-Generation Quark More Massive than the Z0 Boson in ppbar Collisions at sqrt(s) = 1.8 TeV

We present the results of a search for pair production of a fourth-generation charge -1/3 quark (b') in sqrt(s)=1.8 TeV ppbar collisions using 88 pb^(-1) of data obtained with the Collider Detector at Fermilab. We assume that both quarks decay via the flavor-changing neutral current process b' -> bZ and that the b' mass is greater than m_Z + m_b. We studied the decay mode b'b'bar -> ZZ b bbar where one Z0 decays into e^+e^- or mu^+ mu^- and the other decays hadronically, giving a signature of two leptons plus jets. An upper limit on the cross section of ppbar -> b'b'bar times [BR (b' -> bZ)]^2 is established as a function of the b' mass. We exclude at 95% confidence level a b' quark with mass between 100 and 199 GeV/c^2 for BR(b' -> bZ) = 100%.Comment: 12 pages, 2 figures, submitted to Phys. Rev. Letters on 9/12/9

Search for charged Higgs decays of the top quark using hadronic tau decays

We present the result of a search for charged Higgs decays of the top quark, produced in $p\bar{p}$ collisions at $\surd s =$ 1.8 TeV. When the charged Higgs is heavy and decays to a tau lepton, which subsequently decays hadronically, the resulting events have a unique signature: large missing transverse energy and the low-charged-multiplicity tau. Data collected in the period 1992-1993 at the Collider Detector at Fermilab, corresponding to 18.7$\pm$0.7~pb$^{-1}$, exclude new regions of combined top quark and charged Higgs mass, in extensions to the standard model with two Higgs doublets.Comment: uuencoded, gzipped tar file of LaTeX and 6 Postscript figures; 11 pp; submitted to Phys. Rev.